SMTL ID : 6kw1.1

The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.114, H.116, D.118, H.179 Ligands: ZN.2, 9RX.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.116, A:H.179 ZN.2: 7 residues within 4Å: Chain A: H.114, D.118, R.119, C.198, H.240 Ligands: ZN.1, 9RX.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:C.198, A:H.240 ZN.13: 6 residues within 4Å: Chain B: H.114, H.116, D.118, H.179 Ligands: ZN.14, 9RX.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.114, B:H.116, B:H.179 ZN.14: 7 residues within 4Å: Chain B: H.114, D.118, R.119, C.198, H.240 Ligands: ZN.13, 9RX.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.118, B:C.198, B:H.240

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 9 residues within 4Å: Chain A: Y.67, P.68, R.205, H.240 Chain B: D.63, G.64, A.65 Ligands: MG.4, 9RX.6 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: S.161, G.176, A.177, E.218, T.221, S.222, R.225 Ligand excluded by PLIP CL.11: 9 residues within 4Å: Chain A: D.63, G.64, A.65 Chain B: Y.67, P.68, R.205, H.240 Ligands: MG.15, 9RX.16 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain B: G.176, A.177, E.218, T.221, S.222, R.225 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: E.202, R.205, H.240 Chain B: D.63, G.64 Ligands: CL.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.202, H2O.3 MG.15: 5 residues within 4Å: Chain A: G.64 Chain B: E.202, R.205, H.240 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.202

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

NA.5: 1 residues within 4Å: Chain A: D.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.247, A:D.247 Water bridges: A:D.247 NA.9: 5 residues within 4Å: Chain A: D.76, E.79, L.81, R.109, P.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.76, A:D.76, A:R.109, A:R.109 NA.12: 4 residues within 4Å: Chain A: E.202, S.204, L.242 Chain B: G.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.64 Hydrogen bonds: A:E.202 NA.19: 6 residues within 4Å: Chain B: D.76, E.79, L.81, T.108, R.109, P.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.76, B:R.109, B:R.109

2 x 9RX: 2-[3-[2-(1H-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1H-1,2,4-triazol-5-yl]benzoic acid(Non-covalent)

9RX.6: 18 residues within 4Å: Chain A: F.62, Y.67, W.87, H.114, H.116, D.117, D.118, H.179, C.198, Y.201, R.205, G.209, N.210, H.240 Chain B: T.206 Ligands: ZN.1, ZN.2, CL.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.67, A:W.87 Hydrogen bonds: A:N.210, A:N.210 Water bridges: A:D.117, A:H.179, A:H.179 Salt bridges: A:H.179, A:H.240 pi-Stacking: A:F.62, A:F.62, A:H.240 9RX.16: 18 residues within 4Å: Chain B: Q.60, F.62, Y.67, W.87, H.114, H.116, D.117, D.118, H.179, C.198, Y.201, R.205, G.209, N.210, H.240 Ligands: CL.11, ZN.13, ZN.14 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.62, B:Y.67, B:W.87 Hydrogen bonds: B:W.87, B:N.210, B:N.210, B:H.240 Water bridges: B:D.117, B:D.117, B:H.179, B:H.179 Salt bridges: B:H.179, B:H.240 pi-Stacking: B:F.62, B:F.62, B:H.240

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: L.96, P.106, V.107, A.129, V.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.107 Water bridges: A:A.129 ACT.17: 5 residues within 4Å: Chain B: L.96, P.106, V.107, A.129, V.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.107, B:V.107

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

FMT.10: 4 residues within 4Å: Chain A: R.109, R.166, F.167, G.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.109, A:G.168 FMT.20: 1 residues within 4Å: Chain B: R.262 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, Y. et al., Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-beta-Lactamase 2 (VIM-2) Inhibitor. Biomolecules (2020)

Release Date

2020-09-09

Peptides

Beta-lactamase class B VIM-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase class B VIM-2

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