› 1you

X-ray diffraction
2.3Å resolution

Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor

Released:
DOI: 10.2210/pdb1you/pdb
PDB entry 1you coloured by chain, front view.
PDB entry 1you coloured by chain, side view.
PDB entry 1you coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Potent pyrimidinetrione-based inhibitors of MMP-13 with enhanced selectivity over MMP-14.
Blagg JA, Noe MC, Wolf-Gouveia LA, Reiter LA, Laird ER, Chang SP, Danley DE, Downs JT, Elliott NC, Eskra JD, Griffiths RJ, Hardink JR, Haugeto AI, Jones CS, Liras JL, Lopresti-Morrow LL, Mitchell PG, Pandit J, Robinson RP, Subramanyam C, Vaughn-Bowser ML, Yocum SA
Bioorg Med Chem Lett 15 1807-10 (2005)
PMID: 15780611

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
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: 168 amino acids
Theoretical weight: 18.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45452 (Residues: 104-271; Coverage: 37%)
Gene name: MMP13
Sequence domains: Matrixin
Structure domains: Collagenase (Catalytic Domain)

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 2 x CA
Ligand SO4 3 x SO4
Ligand PFD 2 x PFD
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P21212
Unit cell:
a: 81.089Å b: 108.223Å c: 36.035Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.208 0.295
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Matrix metalloproteinases (MMPs): chemical-biological functions and (Q)SARs.
Verma et al. (2007)
8 more

1 mention without citation

Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.
Giangreco et al. (2010)