Structure of PDB 4l19 Chain B Binding Site BS05

Receptor Information
>4l19 Chain B (length=170) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPGDEDP
Ligand information
Ligand ID1UA
InChIInChI=1S/C15H16N2OS/c1-10-5-7-11(8-6-10)9-19-15-16-13-4-2-3-12(13)14(18)17-15/h5-8H,2-4,9H2,1H3,(H,16,17,18)
InChIKeySEZPRMPVJMVCBV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(CSC2=NC3=C(CCC3)C(=O)N2)cc1
ACDLabs 12.01O=C2C3=C(N=C(SCc1ccc(cc1)C)N2)CCC3
OpenEye OEToolkits 1.7.6Cc1ccc(cc1)CSC2=NC3=C(CCC3)C(=O)N2
FormulaC15 H16 N2 O S
Name2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one
ChEMBLCHEMBL1371684
DrugBank
ZINCZINC000006531058
PDB chain4l19 Chain B Residue 309 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4l19 Characterization of selective exosite-binding inhibitors of matrix metalloproteinase 13 that prevent articular cartilage degradation in vitro.
Resolution1.66 Å
Binding residue
(original residue number in PDB)		H222 L239 F241 I243 Y244 T245 P255
Binding residue
(residue number reindexed from 1)		H119 L136 F138 I140 Y141 T142 P152
Annotation score1
Binding affinityMOAD: Ki=0.8uM
BindingDB: IC50=2400nM,Ki=824nM
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:4l19, PDBe:4l19, PDBj:4l19
PDBsum4l19
PubMed25330343
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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