Glyco Property List
Pooled literature properties (glycanDB). Optional filters: ?dataset=uv_vis&property_key=...
GET /api/gdd/glyco-properties/?format=api&page=32
{ "count": 839, "next": "http://glycodata.org/api/gdd/glyco-properties/?format=api&page=33", "previous": "http://glycodata.org/api/gdd/glyco-properties/?format=api&page=31", "results": [ { "id": 621, "dataset": "heparin", "entity": "fondaparinux", "entity_group": "", "entity_class": "synthetic", "property": "anti-Xa activity", "property_key": "anti_xa_activity", "value": "700", "unit": "IU/mg", "value_reported": "700", "unit_reported": "IU/mg", "method": "Review", "method_detail": "synthetic pentasaccharide anti-Xa specific activity", "conditions": "synthetic pentasaccharide anti-Xa specific activity", "conditions_detail": "synthetic pentasaccharide anti-Xa specific activity", "doi": "10.1007/s11239-006-5579-4", "source_url": "https://doi.org/10.1007/s11239-006-5579-4", "year": "2006", "confidence": "medium", "comments": "\"Fondaparinux is a synthetic pentasaccharide, which binds to antithrombin, thereby indirectly selectively inhibiting factor Xa.\" — Fondaparinux anti-Xa ~700 IU/mg is widely cited; this source confirms its selective anti-Xa mechanism. Corroborates existing dataset records. [Bauer KA, 2006, confidence: medium]" }, { "id": 622, "dataset": "heparin", "entity": "heparin", "entity_group": "", "entity_class": "heparin (UFH)", "property": "charge density", "property_key": "charge_density", "value": "3.7", "unit": "per disaccharide", "value_reported": "3.7", "unit_reported": "per disaccharide", "method": "Review", "method_detail": "negative charges (sulfo + carboxyl groups) per disaccharide", "conditions": "negative charges (sulfo + carboxyl groups) per disaccharide", "conditions_detail": "negative charges (sulfo + carboxyl groups) per disaccharide | comparison: vs chondroitin sulfate S/C ~1, dermatan sulfate S/C ~1, DNA/RNA 1 charge per disaccharide", "doi": "10.3390/molecules22061025", "source_url": "https://doi.org/10.3390/molecules22061025", "year": "2017", "confidence": "high", "comments": "\"Both methods exploit the polymeric nature and uniquely high charge density of heparin (~3.7 negative charges/disaccharide), distinguishing heparin from other biopolymers such as chondroitin sulfate (CS) (S/C ratio of ~1), dermatan sulfate (DS) (S/C ratio of ~1) or DNA/RNA (1 negative charge per disaccharide).\" — Total negative charges (sulfate + carboxylate) per disaccharide for heparin. [van der Meer JY, Kellenbach E, van den Bos L, 2017, confidence: high]" }, { "id": 623, "dataset": "heparin", "entity": "heparin", "entity_group": "", "entity_class": "heparin (UFH)", "property": "charge density", "property_key": "charge_density", "value": "3.3", "unit": "per disaccharide", "value_reported": "3.3", "unit_reported": "per disaccharide", "method": "Review", "method_detail": "negative charges per disaccharide (highest of any known biomolecule)", "conditions": "negative charges per disaccharide (highest of any known biomolecule)", "conditions_detail": "negative charges per disaccharide (highest of any known biomolecule)", "doi": "10.1039/c7ob01058c", "source_url": "https://doi.org/10.1039/c7ob01058c", "year": "2017", "confidence": "high", "comments": "\"Heparin has the highest negative charge density of any known biomolecule (~3.3 negative charges per disaccharide)\" — Same DOI also has a charge_density=3.3 record in existing dataset; retained here with verbatim quote for the negative-charges-per-disaccharide framing. [Weiss RJ, Esko JD, Tor Y, 2017, confidence: high]" }, { "id": 624, "dataset": "heparin", "entity": "heparin", "entity_group": "", "entity_class": "heparin (UFH)", "property": "charge density", "property_key": "charge_density", "value": "2.3", "unit": "per disaccharide", "value_reported": "2.3", "unit_reported": "per disaccharide", "method": "Review", "method_detail": "sulfate groups per disaccharide (heparin)", "conditions": "sulfate groups per disaccharide (heparin)", "conditions_detail": "sulfate groups per disaccharide (heparin) | charge type: sulfate groups only (excludes carboxylate)", "doi": "10.1039/c7ob01058c", "source_url": "https://doi.org/10.1039/c7ob01058c", "year": "2017", "confidence": "high", "comments": "\"heparin is related in structure to HS (2.3 sulfate groups per disaccharide in heparin vs. ~0.8 sulfate groups per disaccharide in typical HS)\" — Sulfates-per-disaccharide (not total charge); add ~1 carboxylate/disaccharide for total charge. [Weiss RJ, Esko JD, Tor Y, 2017, confidence: high]" }, { "id": 625, "dataset": "heparin", "entity": "heparan sulfate (typical)", "entity_group": "", "entity_class": "heparan sulfate", "property": "charge density", "property_key": "charge_density", "value": "0.8", "unit": "per disaccharide", "value_reported": "0.8", "unit_reported": "per disaccharide", "method": "Review", "method_detail": "sulfate groups per disaccharide (typical heparan sulfate)", "conditions": "sulfate groups per disaccharide (typical heparan sulfate)", "conditions_detail": "sulfate groups per disaccharide (typical heparan sulfate) | charge type: sulfate groups only (excludes carboxylate)", "doi": "10.1039/c7ob01058c", "source_url": "https://doi.org/10.1039/c7ob01058c", "year": "2017", "confidence": "high", "comments": "\"2.3 sulfate groups per disaccharide in heparin vs. ~0.8 sulfate groups per disaccharide in typical HS\" — Heparan sulfate sulfates-per-disaccharide (much lower than heparin). [Weiss RJ, Esko JD, Tor Y, 2017, confidence: high]" }, { "id": 626, "dataset": "heparin", "entity": "heparin", "entity_group": "", "entity_class": "heparin (UFH)", "property": "charge density", "property_key": "charge_density", "value": "2.5", "unit": "per disaccharide", "value_reported": "2.5", "unit_reported": "per disaccharide", "method": "Experiment", "method_detail": "average sulfation level (sulfates per disaccharide) from disaccharide composition analysis; ~2.2 measured for porcine mucosal heparin", "conditions": "average sulfation level (sulfates per disaccharide) from disaccharide composition analysis; ~2.2 measured for porcine mucosal heparin", "conditions_detail": "average sulfation level (sulfates per disaccharide) from disaccharide composition analysis; ~2.2 measured for porcine mucosal heparin | range: 1.4-2.5 sulfates per disaccharide (typically high end) | measured PMH: 2.2 | charge type: sulfate groups only", "doi": "10.1038/s41598-019-39093-6", "source_url": "https://doi.org/10.1038/s41598-019-39093-6", "year": "2019", "confidence": "high", "comments": "\"This provides Hp with an overall sulfation level of 1.4-2.5 sulfates per disaccharide unit, but most typically at the higher end of this range\" — Heparin overall sulfation (sulfates per disaccharide); same paper measured ~2.2 for porcine mucosal heparin. [Taylor S, Hogwood J, Guo W, et al., 2019, confidence: high]" }, { "id": 627, "dataset": "heparin", "entity": "heparan sulfate", "entity_group": "", "entity_class": "heparan sulfate", "property": "charge density", "property_key": "charge_density", "value": "0.9", "unit": "per disaccharide", "value_reported": "0.55-1.25", "unit_reported": "per disaccharide", "method": "Review", "method_detail": "typical overall sulfation (sulfates per disaccharide) of heparan sulfate", "conditions": "typical overall sulfation (sulfates per disaccharide) of heparan sulfate", "conditions_detail": "typical overall sulfation (sulfates per disaccharide) of heparan sulfate | charge type: sulfate groups only (excludes carboxylate)", "doi": "10.1038/s41598-019-39093-6", "source_url": "https://doi.org/10.1038/s41598-019-39093-6", "year": "2019", "confidence": "high", "comments": "\"HS ... usually comprises much longer chains. HS possesses higher ratios of GlcA/IdoA and GlcNAc/GlcNS compared to Hp, and lower overall sulfation (typically 0.55-1.25 sulfates per disaccharide).\" — Heparan sulfate overall sulfation range. [Taylor S, Hogwood J, Guo W, et al., 2019, confidence: high]" }, { "id": 628, "dataset": "heparin", "entity": "heparan sulfate (mouse kidney cortex)", "entity_group": "", "entity_class": "heparan sulfate", "property": "charge density", "property_key": "charge_density", "value": "0.79", "unit": "per disaccharide", "value_reported": "0.79", "unit_reported": "per disaccharide", "method": "Experiment", "method_detail": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/+ control mouse kidney", "conditions": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/+ control mouse kidney", "conditions_detail": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/+ control mouse kidney | tissue: mouse kidney cortex (db/+ control) | uncertainty: +/-0.10 SEM | charge type: sulfate groups only", "doi": "10.1369/0022155413494392", "source_url": "https://doi.org/10.1369/0022155413494392", "year": "2013", "confidence": "high", "comments": "\"The amount (mean +/- SEM) of sulfate per disaccharide unit was 0.90 +/- 0.03 for HS from db/db mice and 0.79 +/- 0.10 for HS from db/+ mice\" — Experimentally measured HS sulfate-per-disaccharide (control kidney). [Reine TM, Grondahl F, Jenssen T, et al., 2013, confidence: high]" }, { "id": 629, "dataset": "heparin", "entity": "heparan sulfate (mouse kidney cortex, diabetic db/db)", "entity_group": "", "entity_class": "heparan sulfate", "property": "charge density", "property_key": "charge_density", "value": "0.9", "unit": "per disaccharide", "value_reported": "0.9", "unit_reported": "per disaccharide", "method": "Experiment", "method_detail": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/db diabetic mouse kidney", "conditions": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/db diabetic mouse kidney", "conditions_detail": "sulfate per disaccharide by RPIP-HPLC disaccharide analysis of HS from db/db diabetic mouse kidney | tissue: mouse kidney cortex (db/db diabetic) | uncertainty: +/-0.03 SEM | charge type: sulfate groups only", "doi": "10.1369/0022155413494392", "source_url": "https://doi.org/10.1369/0022155413494392", "year": "2013", "confidence": "high", "comments": "\"The amount (mean +/- SEM) of sulfate per disaccharide unit was 0.90 +/- 0.03 for HS from db/db mice and 0.79 +/- 0.10 for HS from db/+ mice\" — Experimentally measured HS sulfate-per-disaccharide (diabetic kidney); no significant difference vs control. [Reine TM, Grondahl F, Jenssen T, et al., 2013, confidence: high]" }, { "id": 630, "dataset": "heparin", "entity": "heparin (Anodonta anodonta, slow-moving high-MW component)", "entity_group": "", "entity_class": "heparinoid (other)", "property": "charge density", "property_key": "charge_density", "value": "2.66", "unit": "per disaccharide", "value_reported": "2.66", "unit_reported": "per disaccharide", "method": "Experiment", "method_detail": "sulfate-to-carboxyl (S/C) ratio of the high-MW heparin component from freshwater mollusc, by oligosaccharide mapping", "conditions": "sulfate-to-carboxyl (S/C) ratio of the high-MW heparin component from freshwater mollusc, by oligosaccharide mapping", "conditions_detail": "sulfate-to-carboxyl (S/C) ratio of the high-MW heparin component from freshwater mollusc, by oligosaccharide mapping | source species: Anodonta anodonta (freshwater mollusc) | Mr: 14900 | metric: sulfate-to-carboxyl ratio", "doi": "10.1021/bm0505033", "source_url": "https://doi.org/10.1021/bm0505033", "year": "2005", "confidence": "high", "comments": "\"The first species had an Mr of about 14 900 and a sulfate-to-carboxyl ratio of 2.66, while the second heparin component had an Mr of 7920 and a charge density of 2.11.\" — Mollusc-derived heparin; S/C ratio (sulfates per carboxyl ~= sulfates per disaccharide since 1 carboxyl/disaccharide). [Volpi N, Maccari F, 2005, confidence: high]" }, { "id": 631, "dataset": "heparin", "entity": "heparin (Anodonta anodonta, fast-moving low-MW component)", "entity_group": "", "entity_class": "heparinoid (other)", "property": "charge density", "property_key": "charge_density", "value": "2.11", "unit": "per disaccharide", "value_reported": "2.11", "unit_reported": "per disaccharide", "method": "Experiment", "method_detail": "charge density (sulfate per disaccharide) of the low-MW heparin component from freshwater mollusc", "conditions": "charge density (sulfate per disaccharide) of the low-MW heparin component from freshwater mollusc", "conditions_detail": "charge density (sulfate per disaccharide) of the low-MW heparin component from freshwater mollusc | source species: Anodonta anodonta (freshwater mollusc) | Mr: 7920 | metric: charge density (S per disaccharide)", "doi": "10.1021/bm0505033", "source_url": "https://doi.org/10.1021/bm0505033", "year": "2005", "confidence": "high", "comments": "\"the second heparin component had an Mr of 7920 and a charge density of 2.11.\" — Lower-sulfated mollusc heparin component. [Volpi N, Maccari F, 2005, confidence: high]" }, { "id": 632, "dataset": "heparin", "entity": "heparin (free acid, amorphous preparations)", "entity_group": "", "entity_class": "heparin (UFH)", "property": "sulfur content", "property_key": "sulfur_content", "value": "13.5", "unit": "% sulfur", "value_reported": "13.5", "unit_reported": "% sulfur", "method": "Experiment", "method_detail": "elemental sulphur analysis of amorphous heparin free acid (classic fractionation study)", "conditions": "elemental sulphur analysis of amorphous heparin free acid (classic fractionation study)", "conditions_detail": "elemental sulphur analysis of amorphous heparin free acid (classic fractionation study) | form: free acid, amorphous | basis: % S by mass | qualifier: up to", "doi": "10.1042/bj0330047", "source_url": "https://doi.org/10.1042/bj0330047", "year": "1939", "confidence": "high", "comments": "\"the amorphous preparations can contain 20 % more S (up to 13.5 % in the free acid) than the crystalline product, which has 11.5 %.\" — Highest %S for amorphous heparin free acid (classic elemental-analysis paper). [Jorpes E, Bergstrom S, 1939, confidence: high]" }, { "id": 633, "dataset": "heparin", "entity": "heparin (crystalline barium salt-derived free acid)", "entity_group": "", "entity_class": "heparin (UFH)", "property": "sulfur content", "property_key": "sulfur_content", "value": "11.5", "unit": "% sulfur", "value_reported": "11.5", "unit_reported": "% sulfur", "method": "Experiment", "method_detail": "elemental sulphur analysis of crystalline heparin product (free acid)", "conditions": "elemental sulphur analysis of crystalline heparin product (free acid)", "conditions_detail": "elemental sulphur analysis of crystalline heparin product (free acid) | form: crystalline product, free acid | basis: % S by mass", "doi": "10.1042/bj0330047", "source_url": "https://doi.org/10.1042/bj0330047", "year": "1939", "confidence": "high", "comments": "\"the amorphous preparations can contain 20 % more S (up to 13.5 % in the free acid) than the crystalline product, which has 11.5 %.\" — %S of crystalline heparin product. [Jorpes E, Bergstrom S, 1939, confidence: high]" }, { "id": 634, "dataset": "heparin", "entity": "heparin (liver, fractionated preparations)", "entity_group": "", "entity_class": "heparin (UFH)", "property": "sulfur content", "property_key": "sulfur_content", "value": "9.629999999999999", "unit": "% sulfur", "value_reported": "7-12.26", "unit_reported": "% sulfur", "method": "Experiment", "method_detail": "elemental sulphur analysis range across liver heparin fractions, correlated with anticoagulant potency", "conditions": "elemental sulphur analysis range across liver heparin fractions, correlated with anticoagulant potency", "conditions_detail": "elemental sulphur analysis range across liver heparin fractions, correlated with anticoagulant potency | source: liver | basis: % S by mass | potency range: 45-160% of standard", "doi": "10.1042/bj0330047", "source_url": "https://doi.org/10.1042/bj0330047", "year": "1939", "confidence": "high", "comments": "\"Preparations of liver heparin containing from 7 to 12 26 % S show potencies varying from 45 to 160 % of the activity of the standard heparin from which they are derived.\" — Liver heparin %S range; '12 26' in OCR is 12.26%. Anticoagulant potency rises with sulfur content. [Jorpes E, Bergstrom S, 1939, confidence: high]" }, { "id": 635, "dataset": "heparin", "entity": "supersulfated heparin (depolymerized)", "entity_group": "", "entity_class": "heparinoid (other)", "property": "sulfur content", "property_key": "sulfur_content", "value": "13.56", "unit": "% sulfur", "value_reported": "13.56", "unit_reported": "% sulfur", "method": "Experiment", "method_detail": "elemental analysis (sodium salt) of depolymerized and supersulfated heparin", "conditions": "elemental analysis (sodium salt) of depolymerized and supersulfated heparin", "conditions_detail": "elemental analysis (sodium salt) of depolymerized and supersulfated heparin | form: sodium salt | modification: depolymerized + supersulfated | basis: % S by mass", "doi": "", "source_url": "https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/4727063", "year": "1988", "confidence": "medium", "comments": "\"depolymerized and supersulfated sodium heparin ... elemental analysis showing S: 13.56%\" — Patent elemental analysis of a supersulfated heparin (no DOI; US patent). Higher than native heparin due to extra sulfation. [US Patent 4727063, 1988, confidence: medium]" }, { "id": 636, "dataset": "heparin", "entity": "heparin pentasaccharide (fondaparinux)", "entity_group": "", "entity_class": "synthetic", "property": "protein binding affinity (Kd)", "property_key": "binding_affinity", "value": "0.022", "unit": "µM", "value_reported": "22.0", "unit_reported": "nM", "method": "Experiment", "method_detail": "Kd vs antithrombin (AT), measured by enhancement of AT intrinsic fluorescence (ex 280 nm, em 340 nm) on fondaparinux binding", "conditions": "Kd vs antithrombin (AT), measured by enhancement of AT intrinsic fluorescence (ex 280 nm, em 340 nm) on fondaparinux binding", "conditions_detail": "Kd vs antithrombin (AT), measured by enhancement of AT intrinsic fluorescence (ex 280 nm, em 340 nm) on fondaparinux binding | partner: antithrombin III | technique: fluorescence | temperature C: 25", "doi": "10.1074/jbc.M113.485268", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3764794/", "year": "2013", "confidence": "high", "comments": "\"Fondaparinux bound to antithrombin with a KD of 22.0 ± 3.4 nM\" — Synthetic AT-binding pentasaccharide (fondaparinux); canonical AT-III interaction [Viskov C, Just M, Laux V, Mourier P, Lorenz M, et al., 2013, confidence: high]" }, { "id": 637, "dataset": "heparin", "entity": "heparin pentasaccharide (fondaparinux)", "entity_group": "", "entity_class": "synthetic", "property": "protein binding affinity (Kd)", "property_key": "binding_affinity", "value": "0.0207", "unit": "µM", "value_reported": "0.0207", "unit_reported": "µM", "method": "Experiment", "method_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl", "conditions": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl", "conditions_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl | partner: antithrombin III | technique: fluorescence | NaCl M: 0.1 | temperature C: 25", "doi": "10.1074/jbc.M113.485268", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3764794/", "year": "2013", "confidence": "high", "comments": "\"The Kd values obtained for fondaparinux ... 0.0207 µM at 0.1 M NaCl\" — Fondaparinux/AT Kd at low salt; Table 3 [Viskov C, Just M, Laux V, Mourier P, Lorenz M, et al., 2013, confidence: high]" }, { "id": 638, "dataset": "heparin", "entity": "heparin pentasaccharide (fondaparinux)", "entity_group": "", "entity_class": "synthetic", "property": "protein binding affinity (Kd)", "property_key": "binding_affinity", "value": "0.279", "unit": "µM", "value_reported": "0.279", "unit_reported": "µM", "method": "Experiment", "method_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.25 M NaCl", "conditions": "Kd vs antithrombin (AT) by fluorescence titration at 0.25 M NaCl", "conditions_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.25 M NaCl | partner: antithrombin III | technique: fluorescence | NaCl M: 0.25 | temperature C: 25", "doi": "10.1074/jbc.M113.485268", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3764794/", "year": "2013", "confidence": "high", "comments": "\"Kd values obtained for fondaparinux ... 0.279 µM at 0.25 M NaCl\" — Fondaparinux/AT Kd at physiological salt; Table 3. Ionic strength markedly weakens affinity [Viskov C, Just M, Laux V, Mourier P, Lorenz M, et al., 2013, confidence: high]" }, { "id": 639, "dataset": "heparin", "entity": "heparin pentasaccharide (fondaparinux)", "entity_group": "", "entity_class": "synthetic", "property": "protein binding affinity (Kd)", "property_key": "binding_affinity", "value": "3.47", "unit": "µM", "value_reported": "3.47", "unit_reported": "µM", "method": "Experiment", "method_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.5 M NaCl", "conditions": "Kd vs antithrombin (AT) by fluorescence titration at 0.5 M NaCl", "conditions_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.5 M NaCl | partner: antithrombin III | technique: fluorescence | NaCl M: 0.5 | temperature C: 25", "doi": "10.1074/jbc.M113.485268", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3764794/", "year": "2013", "confidence": "high", "comments": "\"Kd values obtained for fondaparinux ... 3.47 µM at 0.5 M NaCl\" — Fondaparinux/AT Kd at high salt; Table 3 [Viskov C, Just M, Laux V, Mourier P, Lorenz M, et al., 2013, confidence: high]" }, { "id": 640, "dataset": "heparin", "entity": "heparin dodecasaccharide (two AT-binding pentasaccharides)", "entity_group": "", "entity_class": "heparin oligosaccharide", "property": "protein binding affinity (Kd)", "property_key": "binding_affinity", "value": "0.0099", "unit": "µM", "value_reported": "0.0099", "unit_reported": "µM", "method": "Experiment", "method_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl", "conditions": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl", "conditions_detail": "Kd vs antithrombin (AT) by fluorescence titration at 0.1 M NaCl | partner: antithrombin III | technique: fluorescence | NaCl M: 0.1 | temperature C: 25", "doi": "10.1074/jbc.M113.485268", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3764794/", "year": "2013", "confidence": "high", "comments": "\"Binding of the dodecasaccharide to AT was investigated in the presence of 0.1, 0.25, and 0.5 M NaCl yielding Kd values of 0.0099, 0.086, and 1.23 µM, respectively\" — Dodecasaccharide with two pentasaccharide motifs; 0.1 M NaCl [Viskov C, Just M, Laux V, Mourier P, Lorenz M, et al., 2013, confidence: high]" } ] }