› 3wv3

X-ray diffraction
1.6Å resolution

Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide

Released:
DOI: 10.2210/pdb3wv3/pdb
PDB entry 3wv3 coloured by chain, front view.
PDB entry 3wv3 coloured by chain, side view.
PDB entry 3wv3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thieno[2,3-d]pyrimidine-2-carboxamides bearing a carboxybenzene group at 5-position: highly potent, selective, and orally available MMP-13 inhibitors interacting with the S1″ binding site.
Nara H, Sato K, Naito T, Mototani H, Oki H, Yamamoto Y, Kuno H, Santou T, Kanzaki N, Terauchi J, Uchikawa O, Kori M
Bioorg Med Chem 22 5487-505 (2014)
PMID: 25192810

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-545655 (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

6 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 4 x CA
Ligand NA 2 x NA
Ligand FMT 2 x FMT
Ligand EDO 2 x EDO
Ligand WLL 2 x WLL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: C2
Unit cell:
a: 135.558Å b: 36.352Å c: 95.853Å
α: 90° β: 130.643° γ: 90°
R-values:
R R work R free
0.166 0.163 0.212
Expression system: Escherichia coli

Quick links

Citations

5 review citations

The Rebirth of Matrix Metalloproteinase Inhibitors: Moving Beyond the Dogma.
Fields GB. (2019)
4 more

1 mention without citation

Molecular Dynamics Simulations of Matrix Metalloproteinase 13 and the Analysis of the Specificity Loop and the S1'-Site.
Choi et al. (2023)