Structure of PDB 3kec Chain B Binding Site BS06

Receptor Information
>3kec Chain B (length=167) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPGD
Ligand information
Ligand ID3KE
InChIInChI=1S/C24H21N5O4/c1-33-21-11-7-17(8-12-21)15-29-27-22(26-28-29)19-3-2-4-20(13-19)23(30)25-14-16-5-9-18(10-6-16)24(31)32/h2-13H,14-15H2,1H3,(H,25,30)(H,31,32)
InChIKeyVUTBCSIBPMXNCZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C(O)c1ccc(cc1)CNC(=O)c4cccc(c2nn(nn2)Cc3ccc(OC)cc3)c4
CACTVS 3.352COc1ccc(Cn2nnc(n2)c3cccc(c3)C(=O)NCc4ccc(cc4)C(O)=O)cc1
OpenEye OEToolkits 1.7.0COc1ccc(cc1)Cn2nc(nn2)c3cccc(c3)C(=O)NCc4ccc(cc4)C(=O)O
FormulaC24 H21 N5 O4
Name4-{[({3-[2-(4-methoxybenzyl)-2H-tetrazol-5-yl]phenyl}carbonyl)amino]methyl}benzoic acid;
4-((3-(2-(4-methoxybenzyl)-2H-tetrazol-5-yl)benzamido)methyl)benzoic acid
ChEMBLCHEMBL603623
DrugBank
ZINCZINC000045386357
PDB chain3kec Chain B Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kec Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		K140 N215 F217 L218 H222 L239 F241 P242 I243 Y244 T245 Y246 T247 K249 F252
Binding residue
(residue number reindexed from 1)		K37 N112 F114 L115 H119 L136 F138 P139 I140 Y141 T142 Y143 T144 K146 F149
Annotation score1
Binding affinityMOAD: ic50=58nM
BindingDB: IC50=130nM
Enzymatic activity
Catalytic site (original residue number in PDB) H222 E223 H226 H232
Catalytic site (residue number reindexed from 1) H119 E120 H123 H129
Enzyme Commision number 3.4.24.-
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0031012 extracellular matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kec, PDBe:3kec, PDBj:3kec
PDBsum3kec
PubMed20005097
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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