SMTL ID : 4ivp.1

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN51/20

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x I51: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-5-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

I51.1: 12 residues within 4Å: Chain A: H.13, E.38, W.43, I.52, I.55, Q.80, M.83, Y.87, R.118, A.123, Y.127, R.177 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.127 Hydrogen bonds: A:E.38, A:Q.80, A:Q.80, A:R.118 Water bridges: A:Y.56, A:R.131, A:R.131 pi-Stacking: A:Y.127 I51.4: 11 residues within 4Å: Chain B: H.13, E.38, I.52, I.55, Y.56, Q.80, M.83, Y.87, R.118, A.123, Y.127 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.38, B:Y.56, B:Q.80, B:Q.80, B:R.118 Water bridges: B:Y.56, B:R.131, B:R.131 pi-Stacking: B:Y.127

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

SO4.2: 8 residues within 4Å: Chain A: H.13, G.14, M.15, G.16, K.17, T.18, R.175, R.177 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.14, A:M.15, A:G.16, A:K.17, A:T.18 Salt bridges: A:R.175, A:R.177 SO4.3: 2 residues within 4Å: Chain A: H.60, R.181 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.60, A:R.181 SO4.5: 7 residues within 4Å: Chain B: H.13, G.14, M.15, G.16, K.17, T.18, R.171 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.14, B:M.15, B:G.16, B:K.17, B:T.18, B:T.18, B:R.171 Water bridges: B:K.17, B:K.17 Salt bridges: B:K.17 SO4.6: 3 residues within 4Å: Chain B: K.272, R.275, S.276 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.276, B:S.276 Salt bridges: B:K.272, B:R.275

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

2013-02-06

Peptides

Thymidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidine kinase

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