SMTL ID : 6yt1.1

Mtb TMK crystal structure in complex with compound 26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PK5: 2-ethyl-~{N}-[[4-[4-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]piperidin-1-yl]phenyl]methyl]-1,2,3,5,6,7,8,8~{a}-octahydroimidazo[1,2-a]pyridine-3-carboxamide(Non-covalent)

PK5.1: 15 residues within 4Å: Chain A: D.9, F.36, P.37, Y.39, A.49, L.52, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, Y.165, E.166 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.36, A:P.37, A:L.52, A:F.70, A:Y.103, A:Y.165 Hydrogen bonds: A:R.74, A:R.74, A:N.100 pi-Stacking: A:F.70 PK5.3: 18 residues within 4Å: Chain B: D.9, G.10, F.36, P.37, Y.39, L.52, A.67, F.70, R.74, R.95, Y.96, S.99, N.100, Y.103, L.145, E.170, Q.172 Ligands: CIT.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.36, B:P.37, B:F.70, B:R.95 Hydrogen bonds: B:R.74, B:R.74, B:N.100, B:Q.172 Halogen bonds: B:E.170

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 9 residues within 4Å: Chain A: D.9, G.10, A.11, G.12, K.13, R.14, T.15, D.94, R.95 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14, A:R.95 Water bridges: A:T.15 Salt bridges: A:K.13, A:K.13, A:R.95 CIT.4: 10 residues within 4Å: Chain B: V.8, D.9, G.10, A.11, G.12, K.13, R.14, D.94, R.95 Ligands: PK5.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Water bridges: B:T.15, B:R.95, B:R.95, B:R.95, B:R.95 Salt bridges: B:K.13, B:K.13, B:R.95 CIT.5: 6 residues within 4Å: Chain A: W.119, R.122, R.127 Chain B: E.50, E.55, H.56 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.55 Water bridges: B:H.56, A:R.127 Salt bridges: B:H.56, A:R.122, A:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jian, Y. et al., Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents. Eur.J.Med.Chem. (2020)

Release Date

2020-09-02

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate kinase

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