Structure of PDB 4bak Chain B Binding Site BS03

Receptor Information
>4bak Chain B (length=249) 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
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
Ligand information
Ligand IDM67
InChIInChI=1S/C25H38N6O3/c1-2-13-28-21(32)16-29-22(18-6-4-3-5-7-18)25(34)31-14-12-20(31)24(33)30-15-17-8-10-19(11-9-17)23(26)27/h8-11,18,20,22,29H,2-7,12-16H2,1H3,(H3,26,27)(H,28,32)(H,30,33)/t20-,22+/m0/s1
InChIKeyYEOMROVWVBLQCS-RBBKRZOGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCNC(=O)CNC(C1CCCCC1)C(=O)N2CCC2C(=O)NCc3ccc(cc3)C(=N)N
CACTVS 3.385CCCNC(=O)CN[C@H](C1CCCCC1)C(=O)N2CC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)C(NCC(=O)NCCC)C2CCCCC2)CC3
CACTVS 3.385CCCNC(=O)CN[CH](C1CCCCC1)C(=O)N2CC[CH]2C(=O)NCc3ccc(cc3)C(N)=N
OpenEye OEToolkits 1.9.2[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCN2C(=O)[C@@H](C3CCCCC3)NCC(=O)NCCC)\N
FormulaC25 H38 N6 O3
Name(2S)-N-(4-CARBAMIMIDOYLBENZYL)-1-[(2R)-2-CYCLOHEXYL-2-{[2-OXO-2-(PROPYLAMINO)ETHYL]AMINO}ACETYL]AZETIDINE-2-CARBOXAMIDE
ChEMBL
DrugBank
ZINCZINC000095921231
PDB chain4bak Chain B Residue 1287 [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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PDB4bak Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		H79 Y83 W86 I209 D229 A230 E232 S235 W257 G258 E259 G260 C261
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 I172 D192 A193 E195 S198 W220 G221 E222 G223 C224
Annotation score1
Binding affinityMOAD: Ki=1.22nM
PDBbind-CN: -logKd/Ki=8.91,Ki=1.22nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
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:4bak, PDBe:4bak, PDBj:4bak
PDBsum4bak
PubMed23290007
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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