Structure of PDB 1ets Chain H Binding Site BS01

Receptor Information
>1ets Chain H (length=259) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDI
ALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTT
SVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDA
CEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDRLGS
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 chain1ets Chain H Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ets Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H57 W60D N98 L99 D189 A190 E192 S195 W215 G216 E217 G219 C220
Binding residue
(residue number reindexed from 1)		H43 W50 N95 L96 D199 A200 E202 S205 W227 G228 E229 G230 C231
Annotation score1
Binding affinityMOAD: Ki=6nM
PDBbind-CN: -logKd/Ki=8.22,Ki=6nM
BindingDB: Ki=6nM
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:1ets, PDBe:1ets, PDBj:1ets
PDBsum1ets
PubMed1518046
UniProtP00735|THRB_BOVIN Prothrombin (Gene Name=F2)

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