Structure of PDB 1ba8 Chain B Binding Site BS02

Receptor Information
>1ba8 Chain B (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
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand ID0IT
InChIInChI=1S/C20H30N6O5S/c21-20(22)23-10-4-8-16(13-27)24-18(28)12-26-11-5-9-17(19(26)29)25-32(30,31)14-15-6-2-1-3-7-15/h1-3,6-7,13,16-17,25H,4-5,8-12,14H2,(H,24,28)(H4,21,22,23)/p+1/t16-,17-/m0/s1
InChIKeyWZYFZDIYCCGIQM-IRXDYDNUSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1ccc(cc1)CS(=O)(=O)NC2CCCN(C2=O)CC(=O)NC(CCCNC(=[NH2+])N)C=O
CACTVS 3.385NC(=[NH2+])NCCC[CH](NC(=O)CN1CCC[CH](N[S](=O)(=O)Cc2ccccc2)C1=O)C=O
CACTVS 3.385NC(=[NH2+])NCCC[C@H](NC(=O)CN1CCC[C@H](N[S](=O)(=O)Cc2ccccc2)C1=O)C=O
ACDLabs 12.01O=C(NC(C=O)CCCNC(=[NH2+])\\N)CN2C(=O)C(NS(=O)(=O)Cc1ccccc1)CCC2
OpenEye OEToolkits 1.7.5c1ccc(cc1)CS(=O)(=O)N[C@H]2CCCN(C2=O)CC(=O)N[C@@H](CCCNC(=[NH2+])N)C=O
FormulaC20 H31 N6 O5 S
Nameamino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium;
CVS1578
ChEMBL
DrugBank
ZINC
PDB chain1ba8 Chain B 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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PDB1ba8 Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D E97A L99 I174 D189 A190 S195 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 E94 L96 I172 D192 A193 S198 S219 W220 G221
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.00,Ki=1.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 S198 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:1ba8, PDBe:1ba8, PDBj:1ba8
PDBsum1ba8
PubMed9724521
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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