SMTL ID : 6rmf.1 (1 other biounit)

Crystal structure of NDM-1 with VNRX-5133

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.98, C.182, S.223, H.224 Ligands: K9K.6, K9B.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.182, A:H.224 ZN.2: 6 residues within 4Å: Chain A: H.94, H.96, H.163, T.164 Ligands: K9K.6, K9B.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.163

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

SO4.3: 3 residues within 4Å: Chain A: Q.132, H.133, S.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134 Water bridges: A:Q.132, A:H.133, A:S.134 Salt bridges: A:H.133 SO4.4: 3 residues within 4Å: Chain A: R.208, T.234, R.238 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.208, A:R.238 SO4.5: 1 residues within 4Å: Chain A: K.190 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.190

1 x K9K: (10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide(Non-covalent)

K9K.6: 19 residues within 4Å: Chain A: I.9, V.47, W.67, H.94, H.96, Q.97, D.98, H.163, C.182, K.185, L.192, G.193, N.194, G.196, D.197, H.224 Ligands: ZN.1, ZN.2, K9B.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.67, A:N.194 Hydrogen bonds: A:N.194 Water bridges: A:H.163 Salt bridges: A:H.163, A:K.185, A:H.224

1 x K9B: (4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid(Non-covalent)

K9B.7: 20 residues within 4Å: Chain A: I.9, V.47, W.67, H.94, H.96, Q.97, D.98, K.99, E.126, H.163, C.182, K.185, L.192, G.193, N.194, D.197, H.224 Ligands: ZN.1, ZN.2, K9K.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.67, A:N.194 Hydrogen bonds: A:N.194, A:N.194 Water bridges: A:Q.97, A:H.163 Salt bridges: A:H.163, A:K.185, A:H.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krajnc, A. et al., Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases. J.Med.Chem. (2019)

Release Date

2019-09-11

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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