Structure of PDB 4l19 Chain A Binding Site BS07

Receptor Information
>4l19 Chain A (length=166) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYGPG
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 A Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Y176 A188 F189 H226
Binding residue
(residue number reindexed from 1)		Y73 A85 F86 H123
Annotation score1
Binding affinityMOAD: Ki=0.8uM
PDBbind-CN: -logKd/Ki=6.10,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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4l19, PDBe:4l19, PDBj:4l19
PDBsum4l19
PubMed25330343
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

[Back to BioLiP]