SMTL ID : 7ju8.1 (1 other biounit)

X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.12 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99 CA.4: 7 residues within 4Å: Chain A: A.58, D.59, N.91, Y.92, G.93, D.95 Ligands: FMT.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.1

1 x 9DY: 4-(1,2,3-thiadiazol-4-yl)pyridine(Non-covalent)

9DY.5: 10 residues within 4Å: Chain A: L.82, V.116, H.119, E.120, A.135, L.136, F.138, P.139, I.140, Y.141 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.116, A:H.119, A:Y.141 pi-Stacking: A:H.119

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

FMT.6: 3 residues within 4Å: Chain A: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.13, A:N.14 Water bridges: A:S.11 FMT.7: 3 residues within 4Å: Chain A: I.57, N.91 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.91 Water bridges: A:A.58, A:D.59, A:N.91, A:N.91 FMT.8: 3 residues within 4Å: Chain A: L.53, H.54, D.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.54, A:D.55 FMT.9: 1 residues within 4Å: Chain A: K.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.131 FMT.10: 4 residues within 4Å: Chain A: T.46, P.47, G.166, D.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.167 Water bridges: A:P.47, A:D.167 FMT.12: 7 residues within 4Å: Chain A: A.83, H.84, H.119, E.120, H.123, H.129 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.83, A:A.85

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 5 residues within 4Å: Chain A: Y.73, H.84, A.85, F.86, P.87 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, S.J. et al., Indole Inhibitors of MMP-13 for Arthritic Disorders. Acs Omega (2021)

Release Date

2021-08-04

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Collagenase 3

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