Structure of PDB 4x6m Chain A Binding Site BS01

Receptor Information
>4x6m Chain A (length=238) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVE
SPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLE
TTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKI
PLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVW
HLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Ligand information
Ligand ID3Y3
InChIInChI=1S/C27H26Cl2N8O/c28-19-8-6-17(13-30)18(11-19)14-32-27(38)33-22(10-15-4-2-1-3-5-15)26-34-23(24(29)35-26)16-7-9-20-21(12-16)36-37-25(20)31/h1-9,11-12,22H,10,13-14,30H2,(H,34,35)(H3,31,36,37)(H2,32,33,38)/t22-/m0/s1
InChIKeyPKKLAAQPYSEUAW-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)C[C@@H](c2[nH]c(c(n2)c3ccc4c(c3)[nH]nc4N)Cl)NC(=O)NCc5cc(ccc5CN)Cl
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)N[CH](Cc2ccccc2)c3[nH]c(Cl)c(n3)c4ccc5c(N)n[nH]c5c4
ACDLabs 12.01Clc1cc(c(cc1)CN)CNC(=O)NC(c4nc(c2ccc3c(c2)nnc3N)c(Cl)n4)Cc5ccccc5
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)N[C@@H](Cc2ccccc2)c3[nH]c(Cl)c(n3)c4ccc5c(N)n[nH]c5c4
OpenEye OEToolkits 1.9.2c1ccc(cc1)CC(c2[nH]c(c(n2)c3ccc4c(c3)[nH]nc4N)Cl)NC(=O)NCc5cc(ccc5CN)Cl
FormulaC27 H26 Cl2 N8 O
Name1-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-5-chloro-1H-imidazol-2-yl]-2-phenylethyl}-3-[2-(aminomethyl)-5-chlorobenzyl]urea
ChEMBLCHEMBL3398635
DrugBank
ZINCZINC000115466654
PDB chain4x6m Chain A Residue 301 [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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PDB4x6m Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R39 H40 C42 H57 Y143 I151 D189 A190 C191 K192 G193 S195 T213 S214 W215 G218 G226 V227 Y228
Binding residue
(residue number reindexed from 1)		R26 H27 C29 H44 Y134 I141 D182 A183 C184 K185 G186 S188 T206 S207 W208 G211 G219 V220 Y221
Annotation score1
Binding affinityMOAD: Ki=5.8nM
PDBbind-CN: -logKd/Ki=8.24,Ki=5.8nM
BindingDB: Ki=5.8nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 K192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H44 D93 K185 G186 D187 S188 G189
Enzyme Commision number 3.4.21.27: coagulation factor XIa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4x6m, PDBe:4x6m, PDBj:4x6m
PDBsum4x6m
PubMed25728130
UniProtP03951|FA11_HUMAN Coagulation factor XI (Gene Name=F11)

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