Structure of PDB 2b5t Chain D Binding Site BS01

Receptor Information
>2b5t Chain D (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand IDGU6
InChIInChI=1S/C6H12O15S3/c7-3-2(1-18-22(9,10)11)19-6(8)5(21-24(15,16)17)4(3)20-23(12,13)14/h2-8H,1H2,(H,9,10,11)(H,12,13,14)(H,15,16,17)/t2-,3-,4+,5-,6+/m1/s1
InChIKeyGRHWGVDHRAZFMQ-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O)OS(=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]1O[S](O)(=O)=O
ACDLabs 12.01C1(C(C(OS(=O)(O)=O)C(O)C(COS(=O)(O)=O)O1)OS(O)(=O)=O)O
CACTVS 3.385O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O
OpenEye OEToolkits 1.7.6C(C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O)OS(=O)(=O)O
FormulaC6 H12 O15 S3
Name2,3,6-tri-O-sulfo-alpha-D-glucopyranose;
2,3,6-TRI-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE;
2,3,6-tri-O-sulfo-alpha-D-glucose;
2,3,6-tri-O-sulfo-D-glucose;
2,3,6-tri-O-sulfo-glucose
ChEMBL
DrugBank
ZINCZINC000136252347
PDB chain2b5t Chain G Residue 15 [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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PDB2b5t Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R93 R101 N179
Binding residue
(residue number reindexed from 1)		R89 R98 N177
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 A195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 A198 G199
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2b5t, PDBe:2b5t, PDBj:2b5t
PDBsum2b5t
PubMed16973611
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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