SMTL ID : 5u94.1

Crystal structure of the Mycobacterium tuberculosis PASTA kinase PknB in complex with the potential theraputic kinase inhibitor GSK690693.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x G93: 4-{2-(4-amino-1,2,5-oxadiazol-3-yl)-1-ethyl-7-[(3S)-piperidin-3-ylmethoxy]-1H-imidazo[4,5-c]pyridin-4-yl}-2-methylbut-3 -yn-2-ol(Non-covalent)

G93.1: 23 residues within 4Å: Chain A: L.22, G.23, F.24, V.30, A.43, K.45, E.64, A.65, A.68, V.77, V.79, I.95, M.97, E.98, Y.99, V.100, A.147, N.148, M.150, M.160, D.161, F.162 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.30, A:K.45, A:A.68 Hydrogen bonds: A:F.24, A:K.45, A:E.64, A:E.64, A:E.98, A:V.100, A:D.161, A:F.162 Water bridges: A:F.24

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: D.251, A.254, V.255, Y.268, D.277, R.280, V.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.251, A:Y.268, A:D.277, A:R.280 GOL.3: 6 residues within 4Å: Chain A: P.220, F.221, T.222, Q.232, I.239, R.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.222, A:Q.232 GOL.4: 5 residues within 4Å: Chain A: G.183, T.184, A.185, Q.186, P.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.185, A:Q.186, A:Q.186 GOL.5: 8 residues within 4Å: Chain A: G.102, V.103, I.108, E.112, I.151, S.152, N.155 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:I.151 GOL.6: 8 residues within 4Å: Chain A: I.108, E.112, M.115, R.119, I.151, S.152, N.155 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.119, A:R.119 GOL.7: 8 residues within 4Å: Chain A: E.17, L.18, G.19, E.20, L.32, A.33, R.34, D.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.41 GOL.8: 5 residues within 4Å: Chain A: P.114, M.115, T.116, P.117, H.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.245 GOL.9: 4 residues within 4Å: Chain A: N.72, H.73, P.74, K.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.72, A:K.158

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain A: N.148, D.161 Ligands: G93.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wlodarchak, N. et al., In Silico Screen and Structural Analysis Identifies Bacterial Kinase Inhibitors which Act with beta-Lactams To Inhibit Mycobacterial Growth. Mol. Pharm. (2018)

Release Date

2017-12-20

Peptides

Serine/threonine-protein kinase PknB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein kinase PknB