Structure of PDB 1dwd Chain H Binding Site BS03

Receptor Information
>1dwd Chain H (length=257) 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
QKVIDQF
Ligand information
Ligand IDMID
InChIInChI=1S/C27H31N5O4S/c28-26(29)21-10-8-19(9-11-21)16-24(27(34)32-14-4-1-5-15-32)31-25(33)18-30-37(35,36)23-13-12-20-6-2-3-7-22(20)17-23/h2-3,6-13,17,24,30H,1,4-5,14-16,18H2,(H3,28,29)(H,31,33)/t24-/m1/s1
InChIKeyXXTWZTPVNIYSJZ-XMMPIXPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1)C[C@H](C(=O)N2CCCCC2)NC(=O)CNS(=O)(=O)c3ccc4ccccc4c3)\N
ACDLabs 10.04O=C(N1CCCCC1)C(NC(=O)CNS(=O)(=O)c3cc2ccccc2cc3)Cc4ccc(C(=[N@H])N)cc4
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)CC(C(=O)N2CCCCC2)NC(=O)CNS(=O)(=O)c3ccc4ccccc4c3)N
CACTVS 3.341NC(=N)c1ccc(C[CH](NC(=O)CN[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N4CCCCC4)cc1
CACTVS 3.341NC(=N)c1ccc(C[C@@H](NC(=O)CN[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N4CCCCC4)cc1
FormulaC27 H31 N5 O4 S
Name1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine;
NAPAP
ChEMBLCHEMBL51173
DrugBank
ZINCZINC000003807246
PDB chain1dwd 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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PDB1dwd Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I179 D199 A200 W227 G228
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.18,Ki=6.6nM
BindingDB: Ki=6nM,IC50=690nM,EC50=750nM
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:1dwd, PDBe:1dwd, PDBj:1dwd
PDBsum1dwd
PubMed1939071
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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