SMTL ID : 3wv3.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: FMT.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.4: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.1, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.23, A:D.25, A:D.100

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 6 residues within 4Å: Chain A: A.83, H.119, E.120, H.123, H.129 Ligands: ZN.1 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: Y.73, H.84, A.85, F.86, P.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.85 Water bridges: A:A.85

1 x WLL: N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide(Non-covalent)

WLL.8: 16 residues within 4Å: Chain A: L.82, L.115, V.116, H.119, E.120, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, Y.143, F.149, M.150, P.152 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.119, A:Y.141, A:F.149 Hydrogen bonds: A:A.135, A:T.142, A:T.142, A:T.142 pi-Stacking: A:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nara, H. et al., 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. Bioorg.Med.Chem. (2014)

Release Date

2014-09-24

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Collagenase 3

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