Structure of PDB 1xur Chain A Binding Site BS05

Receptor Information
>1xur Chain A (length=169) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPGDED
Ligand information
Ligand IDPB5
InChIInChI=1S/C18H16N6O2/c25-17(21-10-13-3-1-5-19-8-13)15-7-16(24-12-23-15)18(26)22-11-14-4-2-6-20-9-14/h1-9,12H,10-11H2,(H,21,25)(H,22,26)
InChIKeyNHPBWKYFMTXWAA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c2ncnc(C(=O)NCc1cccnc1)c2)NCc3cccnc3
OpenEye OEToolkits 1.5.0c1cc(cnc1)CNC(=O)c2cc(ncn2)C(=O)NCc3cccnc3
CACTVS 3.341O=C(NCc1cccnc1)c2cc(ncn2)C(=O)NCc3cccnc3
FormulaC18 H16 N6 O2
NameN,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-DICARBOXAMIDE;
PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-[(PYRIDIN-3-YLMETHYL)-AMIDE]
ChEMBLCHEMBL468900
DrugBankDB04761
ZINCZINC000012504499
PDB chain1xur Chain A Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1xur Structural basis for the highly selective inhibition of MMP-13.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		F217 L218 H222 L239 F241 I243 Y244 T245 Y246 T247 K249 S250 F252
Binding residue
(residue number reindexed from 1)		F114 L115 H119 L136 F138 I140 Y141 T142 Y143 T144 K146 S147 F149
Annotation score1
Binding affinityMOAD: ic50=6600nM
PDBbind-CN: -logKd/Ki=5.18,IC50=6600nM
BindingDB: IC50=6600nM
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:1xur, PDBe:1xur, PDBj:1xur
PDBsum1xur
PubMed15734640
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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