SMTL ID : 5nr7.1

Mtb TMK crystal structure in complex with compound 43

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x YUI: 1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione(Non-covalent)

YUI.1: 16 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, A.49, L.52, H.53, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.167, Q.172 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.36, A:P.37, A:L.52, A:F.70, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 Water bridges: A:Q.172 Salt bridges: A:D.9 pi-Stacking: A:H.53, A:F.70 pi-Cation interactions: A:Y.103 YUI.3: 14 residues within 4Å: Chain B: D.9, F.36, P.37, Y.39, A.49, L.52, H.53, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.36, B:P.37, B:A.49, B:L.52, B:L.52, B:F.70 Hydrogen bonds: B:R.74, B:R.74, B:N.100 Salt bridges: B:D.9 pi-Stacking: B:F.70 pi-Cation interactions: B:Y.103

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

CL.2: 5 residues within 4Å: Chain A: V.8, G.10, A.11, G.12, K.13 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: G.10, A.11, G.12, K.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, L. et al., Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors. J. Med. Chem. (2018)

Release Date

2018-03-21

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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