Structure of PDB 3rly Chain H Binding Site BS03

Receptor Information
>3rly 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 IDS29
InChIInChI=1S/C23H29N5O4S/c1-16(27-33(31,32)15-18-6-3-2-4-7-18)23(30)28-13-5-8-20(28)22(29)26-14-17-9-11-19(12-10-17)21(24)25/h2-4,6-7,9-12,16,20,27H,5,8,13-15H2,1H3,(H3,24,25)(H,26,29)/t16-,20+/m1/s1
InChIKeyRXILOHGFTAPEST-UZLBHIALSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(C(=O)N1CCCC1C(=O)NCc2ccc(cc2)C(=N)N)NS(=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.2[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](C)NS(=O)(=O)Cc3ccccc3)\\N
ACDLabs 12.01O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)C(NS(=O)(=O)Cc2ccccc2)C)CCC3
CACTVS 3.370C[CH](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(cc3)C(N)=N
CACTVS 3.370C[C@@H](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
FormulaC23 H29 N5 O4 S
NameN-(benzylsulfonyl)-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
ChEMBLCHEMBL2152431
DrugBank
ZINCZINC000095571883
PDB chain3rly 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3rly Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
Resolution1.51 Å
Binding residue
(original residue number in PDB)		Y60A W60D D189 A190 E192 V213 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		Y47 W50 D192 A193 E195 V218 S219 W220 G221 G223 C224
Annotation score1
Binding affinityBindingDB: Ki=5.2nM
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:3rly, PDBe:3rly, PDBj:3rly
PDBsum3rly
PubMed22612268
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]