SMTL ID : 5dpx.1

1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.84, H.86, H.160 Ligands: L3B.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.84, A:H.86, A:H.160 ZN.2: 4 residues within 4Å: Chain A: D.88, H.89, H.225 Ligands: L3B.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.88, A:H.89, A:H.225 ZN.7: 4 residues within 4Å: Chain B: H.84, H.86, H.160 Ligands: L3B.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.84, B:H.86, B:H.160 ZN.8: 4 residues within 4Å: Chain B: D.88, H.89, H.225 Ligands: L3B.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.88, B:H.89, B:H.225 ZN.11: 4 residues within 4Å: Chain C: H.84, H.86, H.160 Ligands: L3B.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.84, C:H.86, C:H.160 ZN.12: 4 residues within 4Å: Chain C: D.88, H.89, H.225 Ligands: L3B.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.88, C:H.89, C:H.225 ZN.17: 4 residues within 4Å: Chain D: H.84, H.86, H.160 Ligands: L3B.19 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.84, D:H.86, D:H.160 ZN.18: 4 residues within 4Å: Chain D: D.88, H.89, H.225 Ligands: L3B.19 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.88, D:H.89, D:H.225

4 x L3B: 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione(Non-covalent)

L3B.3: 16 residues within 4Å: Chain A: Y.11, H.84, H.86, A.87, D.88, H.89, D.121, F.124, I.128, H.160, S.185, P.189, Y.191, H.225 Ligands: ZN.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.86, A:F.124, A:F.124, A:I.128, A:I.128, A:P.189, A:Y.191 pi-Stacking: A:H.86, A:F.124 L3B.9: 16 residues within 4Å: Chain B: Y.11, H.84, H.86, A.87, D.88, H.89, D.121, F.124, I.128, H.160, S.185, P.189, Y.191, H.225 Ligands: ZN.7, ZN.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.86, B:F.124, B:F.124, B:I.128, B:I.128, B:P.189, B:Y.191 Hydrogen bonds: B:Y.11 pi-Stacking: B:H.86 L3B.13: 16 residues within 4Å: Chain C: Y.11, H.84, H.86, A.87, D.88, H.89, D.121, F.124, I.128, H.160, S.185, P.189, Y.191, H.225 Ligands: ZN.11, ZN.12 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:H.86, C:F.124, C:F.124, C:I.128, C:I.128, C:P.189, C:Y.191 pi-Stacking: C:H.86, C:F.124 L3B.19: 16 residues within 4Å: Chain D: Y.11, H.84, H.86, A.87, D.88, H.89, D.121, F.124, I.128, H.160, S.185, P.189, Y.191, H.225 Ligands: ZN.17, ZN.18 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:H.86, D:F.124, D:F.124, D:I.128, D:I.128, D:P.189, D:Y.191 Hydrogen bonds: D:Y.11 pi-Stacking: D:H.86

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: R.173, A.237, R.238, A.239, G.240, A.241 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.173, A:A.237, A:G.240, A:A.241 Water bridges: A:A.239, A:A.239 SO4.5: 4 residues within 4Å: Chain A: R.137, V.144, I.145, T.146 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.146, A:T.146, A:T.146 Water bridges: A:R.137, A:R.137 Salt bridges: A:R.137 SO4.6: 2 residues within 4Å: Chain A: W.31, R.70 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.70 SO4.10: 4 residues within 4Å: Chain B: R.137, V.144, I.145, T.146 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.146 Water bridges: B:R.137, B:R.137, B:T.146 Salt bridges: B:R.137 SO4.14: 6 residues within 4Å: Chain C: R.173, A.237, R.238, A.239, G.240, A.241 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.173, C:A.237, C:G.240, C:A.241 Water bridges: C:A.239, C:A.239 SO4.15: 4 residues within 4Å: Chain C: R.137, V.144, I.145, T.146 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.146, C:T.146, C:T.146 Water bridges: C:R.137, C:R.137 Salt bridges: C:R.137 SO4.16: 2 residues within 4Å: Chain C: W.31, R.70 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.70 SO4.20: 4 residues within 4Å: Chain D: R.137, V.144, I.145, T.146 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.146 Water bridges: D:R.137, D:R.137, D:T.146 Salt bridges: D:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevaille, L. et al., 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-beta-lactamases. ChemMedChem (2017)

Release Date

2017-01-11

Peptides

Metallo-beta-lactamase L1 type 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Metallo-beta-lactamase L1 type 3

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