SMTL ID : 5nrn.1

Mtb TMK crystal structure in complex with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 95W: 5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione(Non-covalent)

95W.1: 15 residues within 4Å: Chain A: F.36, P.37, Y.39, L.52, M.66, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.107, L.171, Q.172 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.36, A:P.37, A:L.52, A:F.70, A:Y.103, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100 95W.5: 20 residues within 4Å: Chain B: D.9, F.36, P.37, L.52, A.60, M.66, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, R.107, S.150, G.152, R.153, D.168, L.171, Q.172 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.52, B:F.70, B:Y.103, B:Y.103, B:R.153, B:L.171 Hydrogen bonds: B:R.74, B:R.74, B:N.100 Salt bridges: B:D.9 pi-Stacking: B:F.70

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

CL.2: 4 residues within 4Å: Chain A: G.195, A.196, D.197, V.198 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: M.1, C.85 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: W.119, R.122 Chain B: E.55, H.56 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: G.10, A.11, G.12, K.13 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.25, S.30, V.31 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.107, R.153 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: A.49, Q.155, R.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merceron, R. et al., Mtb TMK crystal structure in complex with compound LS3080. To Be Published

Release Date

2018-08-08

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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