SMTL ID : 4jby.1

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with F-SK78

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

FSK.1: 13 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.124, Y.128, R.178 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.81, A:Q.81, A:R.119 Water bridges: A:E.39, A:R.132, A:R.178 pi-Stacking: A:Y.128 FSK.4: 12 residues within 4Å: Chain B: H.14, E.39, W.44, I.53, I.56, Q.81, M.84, Y.88, R.119, A.124, Y.128, R.178 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.128 Hydrogen bonds: B:E.39, B:Q.81, B:Q.81, B:R.119 Water bridges: B:R.132, B:R.132 pi-Stacking: B:Y.128

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

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

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

EDO.8: 3 residues within 4Å: Chain B: H.61, R.62, R.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.62, B:R.62, B:R.182, B:R.182

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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