SMTL ID : 6v1j.1

Structure of KPC-2 bound to QPX7728 at 1.30 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x RM9: (1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid(Covalent)

RM9.1: 13 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, N.166, T.212, R.216, K.230, T.231, G.232, T.233 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.101 Hydrogen bonds: A:S.66, A:S.126, A:S.126, A:T.233, A:T.233 Water bridges: A:K.69, A:K.230, A:T.233, A:T.233 Salt bridges: A:R.216, A:K.230 pi-Stacking: A:W.101, A:W.101

1 x QNA: (1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid(Non-covalent)

QNA.2: 4 residues within 4Å: Chain A: P.103, I.104, K.107, Y.125 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.104, A:Y.125 Water bridges: A:K.107, A:K.107 Salt bridges: A:K.107

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.201, V.204, K.208, A.226, W.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.201, A:K.208, A:K.208 Water bridges: A:Q.201

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

SO4.4: 4 residues within 4Å: Chain A: H.269, S.270, E.271, A.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.269, A:E.271, A:A.272 SO4.5: 2 residues within 4Å: Chain A: T.249, G.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hecker, S.J. et al., Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases. J.Med.Chem. (2020)

Release Date

2020-03-25

Peptides

Carbapenem-hydrolyzing beta-lactamase KPC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carbapenem-hydrolyzing beta-lactamase KPC

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