Structure of PDB 1xud Chain A Binding Site BS05

Receptor Information
>1xud 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 IDPB4
InChIInChI=1S/C22H20F2N4O2/c1-13-7-15(3-5-17(13)23)10-25-21(29)19-9-20(28-12-27-19)22(30)26-11-16-4-6-18(24)14(2)8-16/h3-9,12H,10-11H2,1-2H3,(H,25,29)(H,26,30)
InChIKeyPYFRREJCFXFNRR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc(CNC(=O)c2cc(ncn2)C(=O)NCc3ccc(F)c(C)c3)ccc1F
OpenEye OEToolkits 1.5.0Cc1cc(ccc1F)CNC(=O)c2cc(ncn2)C(=O)NCc3ccc(c(c3)C)F
ACDLabs 10.04O=C(c2ncnc(C(=O)NCc1ccc(F)c(c1)C)c2)NCc3ccc(F)c(c3)C
FormulaC22 H20 F2 N4 O2
NameN,N'-BIS(4-FLUORO-3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE;
PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-(4-FLUORO-3-METHYL-BENZYLAMIDE)
ChEMBLCHEMBL514794
DrugBankDB04760
ZINCZINC000012504498
PDB chain1xud 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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PDB1xud Structural basis for the highly selective inhibition of MMP-13.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		F217 L218 V219 H222 L239 F241 I243 Y244 T245 Y246 T247 S250 F252
Binding residue
(residue number reindexed from 1)		F114 L115 V116 H119 L136 F138 I140 Y141 T142 Y143 T144 S147 F149
Annotation score1
Binding affinityMOAD: ic50=8nM
PDBbind-CN: -logKd/Ki=8.10,IC50=8nM
BindingDB: IC50=8nM
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:1xud, PDBe:1xud, PDBj:1xud
PDBsum1xud
PubMed15734640
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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