SMTL ID : 6yen.1

Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x KJK: (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid(Covalent)

KJK.1: 16 residues within 4Å: Chain A: G.60, S.61, K.64, Q.117, Y.147, N.149, Y.218, N.286, K.312, T.313, G.314, A.315, T.316, G.317, N.343 Ligands: CL.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:S.61, A:Q.117, A:Y.147, A:N.149, A:A.315, A:A.315, A:A.315, A:N.343, A:N.343 Water bridges: A:K.312, A:T.313, A:T.313 Salt bridges: A:K.312

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 4 residues within 4Å: Chain A: Y.37, F.38, T.39, Q.53 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.53

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: W.90, A.157, L.158 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: P.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.1 EDO.5: 4 residues within 4Å: Chain A: G.33, K.34, P.35, Q.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.232 EDO.6: 1 residues within 4Å: Chain A: K.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.49

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.7: 4 residues within 4Å: Chain A: P.137, A.138, W.139, A.140 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.140 Water bridges: A:Q.97, A:Q.97, A:N.99, A:A.140

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain A: H.10 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.10 ZN.9: 2 residues within 4Å: Chain A: T.14, E.18 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.18, H2O.11

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

CL.10: 3 residues within 4Å: Chain A: H.10, R.11 Ligands: ZN.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: V.208, G.317 Ligands: KJK.1 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: E.168, Q.172, W.185, I.186, N.187 Ligand excluded by PLIP

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

NA.13: 1 residues within 4Å: Chain A: D.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, P.A. et al., Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C beta-Lactamase from Escherichia coli . Biomolecules (2020)

Release Date

2020-06-24

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase

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