Structure of PDB 3rm0 Chain H Binding Site BS03

Receptor Information
>3rm0 Chain H (length=251) 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
G
Ligand information
Ligand IDS54
InChIInChI=1S/C25H33N5O4S/c1-17(2)22(29-35(33,34)16-19-7-4-3-5-8-19)25(32)30-14-6-9-21(30)24(31)28-15-18-10-12-20(13-11-18)23(26)27/h3-5,7-8,10-13,17,21-22,29H,6,9,14-16H2,1-2H3,(H3,26,27)(H,28,31)/t21-,22+/m0/s1
InChIKeyBTZOUFLORPKMGE-FCHUYYIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)[CH](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(cc3)C(N)=N
CACTVS 3.370CC(C)[C@@H](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
OpenEye OEToolkits 1.7.2[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](C(C)C)NS(=O)(=O)Cc3ccccc3)\\N
OpenEye OEToolkits 1.7.2CC(C)C(C(=O)N1CCCC1C(=O)NCc2ccc(cc2)C(=N)N)NS(=O)(=O)Cc3ccccc3
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)C(NS(=O)(=O)Cc2ccccc2)C(C)C)CCC3
FormulaC25 H33 N5 O4 S
NameN-(benzylsulfonyl)-D-valyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
ChEMBLCHEMBL1809219
DrugBank
ZINCZINC000072177282
PDB chain3rm0 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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PDB3rm0 Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
Resolution1.34 Å
Binding residue
(original residue number in PDB)		E97A N98 L99 R173 I174 W215 E217
Binding residue
(residue number reindexed from 1)		E94 N95 L96 R171 I172 W220 E222
Annotation score1
Binding affinityBindingDB: Ki=1.29nM
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:3rm0, PDBe:3rm0, PDBj:3rm0
PDBsum3rm0
PubMed22612268
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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