› 5b5p

X-ray diffraction
1.6Å resolution

Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide

Released:
DOI: 10.2210/pdb5b5p/pdb
PDB entry 5b5p coloured by chain, front view.
PDB entry 5b5p coloured by chain, side view.
PDB entry 5b5p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (MMP)-13 Inhibitors with a 1,2,4-Triazol-3-yl Moiety as a Zinc Binding Group Using a Structure-Based Design Approach.
Nara H, Kaieda A, 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 60 608-626 (2017)
PMID: 27966948

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
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: 172 amino acids
Theoretical weight: 19.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P45452 (Residues: 103-274; Coverage: 38%)
Gene name: MMP13
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 6 x CA
Ligand WNN 2 x WNN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2
Unit cell:
a: 135.798Å b: 36.281Å c: 96.382Å
α: 90° β: 130.14° γ: 90°
R-values:
R R work R free
0.175 0.173 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Metalloproteinases and Their Inhibitors: Potential for the Development of New Therapeutics.
Raeeszadeh-Sarmazdeh et al. (2020)
4 more