› 3wv1

X-ray diffraction
1.98Å resolution

Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid

Released:
DOI: 10.2210/pdb3wv1/pdb
PDB entry 3wv1 coloured by chain, front view.
PDB entry 3wv1 coloured by chain, side view.
PDB entry 3wv1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of novel, highly potent, and selective quinazoline-2-carboxamide-based matrix metalloproteinase (MMP)-13 inhibitors without a zinc binding group using a structure-based design approach.
Nara H, Sato K, Naito T, Mototani H, Oki H, Yamamoto Y, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M
J Med Chem 57 8886-902 (2014)
PMID: 25264600

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-155286 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Collagenase 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 171 amino acids
Theoretical weight: 19.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 104-274; Coverage: 38%)
Gene name: MMP13
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

5 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 4 x CA
Ligand NA 2 x NA
Ligand FMT 2 x FMT
Ligand WHH 2 x WHH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: C2
Unit cell:
a: 134.372Å b: 36.058Å c: 95.298Å
α: 90° β: 130.895° γ: 90°
R-values:
R R work R free
0.177 0.175 0.22
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
6 more

5 mentions without citation

A systematic computational analysis of human matrix metalloproteinase 13 (MMP-13) crystal structures and structure-based identification of prospective drug candidates as MMP-13 inhibitors repurposable for osteoarthritis.
Satish Kumar et al. (2020)
4 more