Structure of PDB 3egk Chain H Binding Site BS03

Receptor Information
>3egk Chain H (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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEQPSV
LQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPF
VMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Ligand information
Ligand IDM18
InChIInChI=1S/C20H27ClN2O5/c1-20(2,3)28-19(26)22-12-17(24)23-9-5-8-16(23)13-27-18(25)11-14-6-4-7-15(21)10-14/h4,6-7,10,16H,5,8-9,11-13H2,1-3H3,(H,22,26)/t16-/m0/s1
InChIKeyONXGIEJBNQLITK-INIZCTEOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)(C)OC(=O)NCC(=O)N1CCC[C@H]1COC(=O)Cc2cccc(Cl)c2
ACDLabs 10.04O=C(N1CCCC1COC(=O)Cc2cccc(Cl)c2)CNC(=O)OC(C)(C)C
OpenEye OEToolkits 1.5.0CC(C)(C)OC(=O)NCC(=O)N1CCC[C@H]1COC(=O)Cc2cccc(c2)Cl
CACTVS 3.341CC(C)(C)OC(=O)NCC(=O)N1CCC[CH]1COC(=O)Cc2cccc(Cl)c2
OpenEye OEToolkits 1.5.0CC(C)(C)OC(=O)NCC(=O)N1CCCC1COC(=O)Cc2cccc(c2)Cl
FormulaC20 H27 Cl N2 O5
Name{(2S)-1-[N-(tert-butoxycarbonyl)glycyl]pyrrolidin-2-yl}methyl (3-chlorophenyl)acetate;
(3-Chloro-Phenyl)-acetic acid (S)-1-(2-tert-butoxycarbonylamino-acetyl)-pyrrolidin-2-ylmethyl ester
ChEMBL
DrugBankDB08152
ZINCZINC000039188026
PDB chain3egk Chain H Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3egk KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D L99 A190 C191 V213 W215 G216 G226 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 A191 C192 V216 W218 G219 G229 F230
Annotation score1
Binding affinityMOAD: Ki=22uM
PDBbind-CN: -logKd/Ki=4.66,Ki=22uM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3egk, PDBe:3egk, PDBj:3egk
PDBsum3egk
PubMed17955562
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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