Structure of PDB 2gd4 Chain I Binding Site BS02

Receptor Information
>2gd4 Chain I (length=417) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDICTAKPRDIPMNPMCIYRSPEQKIPEATNRRVWELSKANSRFATTFYQ
HLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEK
TSDQIHFFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISEL
VYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLV
LVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVA
EGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEM
MLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPAASALPGIVAEGRDDLYV
SDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIRE
VPLNTIIFMGRVANPCV
Ligand information
Ligand IDSUS
InChIInChI=1S/C6H13NO14S3/c8-4-2(1-19-23(13,14)15)20-6(9)3(7-22(10,11)12)5(4)21-24(16,17)18/h2-9H,1H2,(H,10,11,12)(H,13,14,15)(H,16,17,18)/t2-,3-,4-,5-,6+/m1/s1
InChIKeyVPSCBZXJXYLJOH-UKFBFLRUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(C1C(C(C(C(O1)O)NS(=O)(=O)O)OS(=O)(=O)O)O)OS(=O)(=O)O
OpenEye OEToolkits 1.7.6C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)NS(=O)(=O)O)OS(=O)(=O)O)O)OS(=O)(=O)O
ACDLabs 12.01N(C1C(OC(C(C1OS(O)(=O)=O)O)COS(=O)(O)=O)O)S(=O)(O)=O
CACTVS 3.385O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O[S](O)(=O)=O)[CH]1N[S](O)(=O)=O
CACTVS 3.385O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O[S](O)(=O)=O)[C@H]1N[S](O)(=O)=O
FormulaC6 H13 N O14 S3
Name2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose;
3,6-di-O-sulfo-N-sulfo-alpha-D-glucosamine;
2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucose;
2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-D-glucose;
2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-glucose
ChEMBL
DrugBank
ZINCZINC000098209427
PDB chain2gd4 Chain F Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2gd4 Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation.
Resolution3.3 Å
Binding residue
(original residue number in PDB)
K11 P12 N45 K114 F122
Binding residue
(residue number reindexed from 1)
K7 P8 N31 K100 F108
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004867 serine-type endopeptidase inhibitor activity
Biological Process
GO:0030193 regulation of blood coagulation
Cellular Component
GO:0005615 extracellular space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:2gd4, PDBe:2gd4, PDBj:2gd4
PDBsum2gd4
PubMed16619025
UniProtP01008|ANT3_HUMAN Antithrombin-III (Gene Name=SERPINC1)

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