SMTL ID : 6d1c.1

Crystal structure of NDM-1 complexed with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.85, H.152, C.171 Ligands: VKE.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.152 ZN.2: 5 residues within 4Å: Chain A: D.87, C.171, H.213 Ligands: VKE.3, ACT.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:C.171, A:H.213

1 x VKE: [(6-oxo-2H,6H-[1,3]dioxolo[4,5-g][1]benzopyran-8-yl)methyl]phosphonic acid(Non-covalent)

VKE.3: 13 residues within 4Å: Chain A: M.30, F.33, V.36, H.83, H.85, D.87, H.152, C.171, N.183, H.213 Ligands: ZN.1, ZN.2, ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183 pi-Stacking: A:F.33

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

ACT.4: 9 residues within 4Å: Chain A: H.152, C.171, K.174, L.181, G.182, N.183, H.213 Ligands: ZN.2, VKE.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.183 Hydrogen bonds: A:N.183 Water bridges: A:K.174 Salt bridges: A:H.152, A:K.174, A:H.213 ACT.5: 7 residues within 4Å: Chain A: A.84, H.85, L.111, E.115, T.153, D.155, D.186 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.115 Hydrogen bonds: A:A.84, A:A.84 Water bridges: A:S.154 Salt bridges: A:H.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pemberton, O.A. et al., Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. (2019)

Release Date

2019-04-17

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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