SMTL ID : 5b5p.2 (1 other biounit)

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

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.120, H.124, H.130 Ligands: WNN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.120, A:H.124, A:H.130 ZN.2: 4 residues within 4Å: Chain A: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:D.72, A:H.85, A:H.98

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.77, G.78, S.80, L.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:S.80, A:L.82, A:D.100, A:E.103 CA.4: 5 residues within 4Å: Chain A: D.60, N.92, Y.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:N.92, A:G.94, A:D.96, H2O.2, H2O.4 CA.5: 4 residues within 4Å: Chain A: T.24, D.26, D.101, E.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.26, A:D.101, A:D.101, A:E.103

1 x WNN: 4-oxo-N-{3-[2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy]benzyl}-3,4-dihydroquinazoline-2-carboxamide(Non-covalent)

WNN.6: 20 residues within 4Å: Chain A: L.83, A.84, L.116, H.120, E.121, H.124, H.130, A.136, L.137, F.139, P.140, I.141, Y.142, T.143, Y.144, T.145, F.150, M.151, P.153 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.120, A:Y.142, A:T.145, A:F.150, A:P.153 Hydrogen bonds: A:E.121, A:A.136, A:T.143, A:T.143, A:T.145 Water bridges: A:G.146 pi-Stacking: A:H.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nara, H. et al., 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. J. Med. Chem. (2017)

Release Date

2017-01-18

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Collagenase 3

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