Structure of PDB 4o97 Chain A Binding Site BS02

Receptor Information
>4o97 Chain A (length=241) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGF
RYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIAL
LELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQ
KGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEA
DGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV
Ligand information
Ligand IDNTX
InChIInChI=1S/C29H34N6O3/c30-23-7-9-24(10-8-23)35-29(36)22-13-25(37-16-18-3-1-5-20(11-18)27(31)32)15-26(14-22)38-17-19-4-2-6-21(12-19)28(33)34/h1-6,11-15,23-24H,7-10,16-17,30H2,(H3,31,32)(H3,33,34)(H,35,36)/t23-,24-
InChIKeyUKPKEJBTCDGYRU-RQNOJGIXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH]1CC[CH](CC1)NC(=O)c2cc(OCc3cccc(c3)C(N)=N)cc(OCc4cccc(c4)C(N)=N)c2
OpenEye OEToolkits 1.7.6c1cc(cc(c1)C(=N)N)COc2cc(cc(c2)OCc3cccc(c3)C(=N)N)C(=O)NC4CCC(CC4)N
OpenEye OEToolkits 1.7.6[H]/N=C(\N)/c1cc(ccc1)COc2cc(cc(c2)C(=O)NC3CCC(CC3)N)OCc4cc(ccc4)/C(=N/[H])/N
ACDLabs 12.01O=C(NC1CCC(N)CC1)c4cc(OCc2cccc(C(=[N@H])N)c2)cc(OCc3cccc(C(=[N@H])N)c3)c4
CACTVS 3.385N[C@H]1CC[C@@H](CC1)NC(=O)c2cc(OCc3cccc(c3)C(N)=N)cc(OCc4cccc(c4)C(N)=N)c2
FormulaC29 H34 N6 O3
NameN-(trans-4-aminocyclohexyl)-3,5-bis[(3-carbamimidoylbenzyl)oxy]benzamide
ChEMBLCHEMBL3289301
DrugBank
ZINC
PDB chain4o97 Chain A Residue 900 [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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PDB4o97 Structure-guided discovery of 1,3,5 tri-substituted benzenes as potent and selective matriptase inhibitors exhibiting in vivo antitumor efficacy.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T98 F99 Q175 D189 S190 C191 Q192 S195 V213 W215 G216
Binding residue
(residue number reindexed from 1)		T93 F94 Q169 D185 S186 C187 Q188 S191 V210 W212 G213
Annotation score1
Binding affinityMOAD: Ki=3nM
PDBbind-CN: -logKd/Ki=8.52,Ki=3nM
BindingDB: Ki=3.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D97 Q188 G189 D190 S191 G192
Enzyme Commision number 3.4.21.109: matriptase.
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:4o97, PDBe:4o97, PDBj:4o97
PDBsum4o97
PubMed24794746
UniProtQ9Y5Y6|ST14_HUMAN Suppressor of tumorigenicity 14 protein (Gene Name=ST14)

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