SMTL ID : 2xx3.1

HUMAN THYMIDYLATE KINASE COMPLEXED WITH thymidine butenyl phosphonate monophosphate and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: V.34, D.35, R.36, A.37, G.38, K.39, S.40, T.41, R.163, G.164, A.165, K.202, S.203, I.204 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.36, A:A.37, A:G.38, A:K.39, A:S.40, A:T.41, A:T.41, A:G.164, A:K.202 Water bridges: A:S.40, A:S.40, A:S.40, A:D.116, A:D.116, A:R.163, A:R.163, A:R.163 Salt bridges: A:K.39 pi-Cation interactions: A:R.163 ADP.5: 15 residues within 4Å: Chain B: V.34, D.35, R.36, A.37, G.38, K.39, S.40, T.41, R.163, G.164, A.165, K.202, S.203, I.204 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.36, B:A.37, B:G.38, B:K.39, B:S.40, B:T.41, B:T.41, B:G.164, B:K.202 Water bridges: B:S.40, B:S.40, B:S.40, B:D.116, B:D.116, B:R.163, B:R.163, B:R.163 Salt bridges: B:K.39 pi-Cation interactions: B:R.163

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.40, D.116 Ligands: ADP.1, TAE.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.40, H2O.1, H2O.1, H2O.1, H2O.4 MG.6: 4 residues within 4Å: Chain B: S.40, D.116 Ligands: ADP.5, TAE.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.40, H2O.9, H2O.9, H2O.9, H2O.12

2 x TAE: N1-[(E)-4-DIHYDROXYPHOSPHONYL-BUT-2-ENYL]-THYMINE(Non-covalent)

TAE.3: 13 residues within 4Å: Chain A: F.62, P.63, R.65, F.92, R.96, R.117, Y.118, G.122, F.125, H.168, R.170, Y.171 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.62, A:F.92 Hydrogen bonds: A:R.65, A:R.65, A:R.96, A:R.96, A:H.168, A:R.170, A:R.170 Water bridges: A:S.40, A:T.126, A:H.168 Salt bridges: A:R.65, A:R.117, A:H.168, A:R.170 pi-Stacking: A:F.92 TAE.7: 13 residues within 4Å: Chain B: F.62, P.63, R.65, F.92, R.96, R.117, Y.118, G.122, F.125, H.168, R.170, Y.171 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.62, B:F.92 Hydrogen bonds: B:R.65, B:R.65, B:R.96, B:R.96, B:H.168, B:R.170, B:R.170, B:Y.171 Water bridges: B:S.40, B:H.168 Salt bridges: B:R.65, B:R.117, B:H.168, B:R.170 pi-Stacking: B:F.92

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 5 residues within 4Å: Chain A: F.152, Q.154, L.155, L.181, H.185 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.155, A:L.155 NO3.8: 5 residues within 4Å: Chain B: F.152, Q.154, L.155, L.181, H.185 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.155, B:L.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Topalis, D. et al., Novel Antiviral C5-Substituted Pyrimidine Acyclic Nucleoside Phosphonates Selected as Human Thymidylate Kinase Substrates. J.Med.Chem. (2011)

Release Date

2011-12-07

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE