ISDA

Deposition Date 2014-05-12

Release Date 2014-09-24

Last Version Date 2023-11-08

Entry Detail

PDB ID:

3WV3

Keywords:

HYDROLASE/HYDROLASE INHIBITOR

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.60 Å

R-Value Free:

0.21

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Collagenase 3
Gene (Uniprot):MMP13
Chain IDs:A, B
Chain Length:171
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P45452 Pfam ID:PF00413 EC:3.4.24.17

Ligand Molecules

EDO

FMT

WLL

Primary Citation

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.Show

Bioorg.Med.Chem. 22 5487 5505 (2014)

PMID: 25192810 DOI: 10.1016/j.bmc.2014.07.025

Abstact

On the basis of X-ray co-crystal structures of matrix metalloproteinase-13 (MMP-13) in complex with its inhibitors, our structure-based drug design (SBDD) strategy was directed to achieving high affinity through optimal protein-ligand interaction with the unique S1″ hydrophobic specificity pocket. This report details the optimization of lead compound 44 to highly potent and selective MMP-13 inhibitors based on fused pyrimidine scaffolds represented by the thienopyrimidin-4-one 26c. Furthermore, we have examined the release of collagen fragments from bovine nasal cartilage in response to a combination of IL-1 and oncostatin M.

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Primary Citation of related structures