SMTL ID : 6oi9.1

Crystal Structure of E. coli Biotin Carboxylase Complexed with 7-[3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x MQM: 7-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine(Non-covalent)

MQM.1: 17 residues within 4Å: Chain A: V.151, I.177, K.179, G.186, M.189, E.221, K.222, Y.223, L.224, H.229, Q.253, H.256, E.296, L.298, I.307, E.308, I.457 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.298, A:I.457 Hydrogen bonds: A:K.179, A:K.222, A:L.224, A:E.296 Salt bridges: A:E.221 MQM.4: 16 residues within 4Å: Chain B: I.177, K.179, G.186, M.189, E.221, K.222, Y.223, L.224, H.229, Q.253, H.256, E.296, L.298, I.307, E.308, I.457 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.298, B:L.298, B:I.457 Hydrogen bonds: B:K.179, B:K.222, B:L.224, B:E.296 Salt bridges: B:E.221

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

EDO.2: 4 residues within 4Å: Chain A: H.256, Q.257, K.258, R.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.258, A:R.358, A:R.358 EDO.3: 7 residues within 4Å: Chain A: I.140, G.153, S.154, D.155, G.156, Y.219, M.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.155, A:G.156 Water bridges: A:V.137 EDO.5: 5 residues within 4Å: Chain B: P.380, G.381, G.382, V.385, W.387 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.382, B:G.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, L.D. et al., Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase. J.Med.Chem. (2019)

Release Date

2019-07-31

Peptides

Biotin carboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biotin carboxylase