Structure of PDB 1hdt Chain H Binding Site BS02

Receptor Information
>1hdt Chain H (length=259) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQFGE
Ligand information
Ligand ID0E7
InChIInChI=1S/C28H38N6O6/c1-18(35)24(26(38)33-22(27(39)40-2)17-20-12-7-4-8-13-20)34-25(37)21(16-19-10-5-3-6-11-19)32-23(36)14-9-15-31-28(29)30/h3-8,10-13,18,21-22,24,35H,9,14-17H2,1-2H3,(H,32,36)(H,33,38)(H,34,37)(H4,29,30,31)/t18-,21-,22-,24-/m0/s1
InChIKeyQKSIUCFYHKTUCL-CKLTXHEASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5CC(C(C(=O)NC(Cc1ccccc1)C(=O)OC)NC(=O)C(Cc2ccccc2)NC(=O)CCCNC(=N)N)O
CACTVS 3.385COC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)[C@H](Cc2ccccc2)NC(=O)CCCNC(N)=N)[C@H](C)O
ACDLabs 12.01O=C(NC(C(=O)NC(C(=O)NC(C(=O)OC)Cc1ccccc1)C(O)C)Cc2ccccc2)CCCNC(=[N@H])N
CACTVS 3.385COC(=O)[CH](Cc1ccccc1)NC(=O)[CH](NC(=O)[CH](Cc2ccccc2)NC(=O)CCCNC(N)=N)[CH](C)O
OpenEye OEToolkits 1.7.5[H]/N=C(\N)/NCCCC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H]([C@H](C)O)C(=O)N[C@@H](Cc2ccccc2)C(=O)OC
FormulaC28 H38 N6 O6
Namemethyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate;
BMS-183507
ChEMBL
DrugBank
ZINCZINC000068735452
PDB chain1hdt Chain H Residue 1 [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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PDB1hdt Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D D189 A190 C191 E192 S195 S214 W215 G216 E217 G219 C220
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 D199 A200 C201 E202 S205 S226 W227 G228 E229 G230 C231
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.76,Ki=17.2nM
Enzymatic activity
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:1hdt, PDBe:1hdt, PDBj:1hdt
PDBsum1hdt
PubMed7853394
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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