SMTL ID : 4jbx.1

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with SK-78

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x SK7: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

SK7.1: 14 residues within 4Å: Chain A: H.14, E.39, W.44, I.53, I.56, Y.57, Q.81, M.84, Y.88, R.119, A.123, A.124, Y.128, R.178 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.39, A:Q.81, A:Q.81, A:R.119 Water bridges: A:R.132, A:R.132 pi-Stacking: A:Y.128 SK7.5: 12 residues within 4Å: Chain B: H.14, E.39, W.44, I.53, I.56, Y.57, Q.81, M.84, Y.88, R.119, A.124, Y.128 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.128 Hydrogen bonds: B:Q.81, B:Q.81, B:R.119, B:R.132 pi-Stacking: B:Y.128

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: H.14, G.15, G.17, R.176, R.178 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.15, A:G.17, A:R.119 Water bridges: A:M.16, A:M.16 Salt bridges: A:R.176, A:R.178 SO4.3: 3 residues within 4Å: Chain A: H.61, R.62, R.182 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.61, A:R.62, A:R.182 SO4.4: 3 residues within 4Å: Chain A: K.18, R.168, R.172 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.18, A:R.168, A:R.172 SO4.6: 7 residues within 4Å: Chain B: H.14, G.15, M.16, G.17, K.18, T.19, R.172 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.15, B:M.16, B:G.17, B:K.18, B:T.19, B:T.19, B:R.172 Water bridges: B:K.18, B:K.18, B:K.18, B:K.18, B:T.20, B:R.172 Salt bridges: B:K.18 SO4.7: 3 residues within 4Å: Chain B: K.273, R.276, S.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.277, B:S.277 Salt bridges: B:K.273, B:R.276 SO4.8: 3 residues within 4Å: Chain B: R.172, K.175, R.176 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.175, B:R.176

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 2 residues within 4Å: Chain B: A.290, R.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.293, B:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pernot, L. et al., New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer. To be Published

Release Date

2013-03-06

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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