SMTL ID : 2yof.3 (2 other biounits)

Plasmodium falciparum thymidylate kinase in complex with a (thio)urea- beta-deoxythymidine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x 74W: 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]thiourea

74W.1: 14 residues within 4Å: Chain A: D.17, F.44, P.45, R.47, L.59, F.74, R.78, R.99, Y.100, S.103, G.104, Y.107, E.151, Y.153 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.44, A:R.99, A:Y.107 Hydrogen bonds: A:D.17, A:R.47, A:R.78, A:R.78 Water bridges: A:D.17, A:D.17, A:S.75, A:R.99, A:G.104, A:S.108, A:E.151, A:Y.153, A:E.154 pi-Stacking: A:F.74

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: L.42, Y.43, F.44, N.46, H.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.43 Salt bridges: A:H.81 ACT.3: 9 residues within 4Å: Chain A: L.16, D.17, R.18, S.19, G.20, K.21, S.22, Y.148 Ligands: ACT.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.19, A:G.20, A:K.21 Water bridges: A:D.17, A:S.22, A:D.98, A:R.99 Salt bridges: A:K.21 ACT.4: 6 residues within 4Å: Chain A: G.20, S.22, T.23, R.145, Y.148 Ligands: ACT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.22, A:T.23, A:T.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, H. et al., Synthesis and Evaluation of Alpha-Thymidine Analogues as Novel Antimalarials. J.Med.Chem. (2012)

Release Date

2013-07-24

Peptides

THYMIDYLATE KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

THYMIDYLATE KINASE

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