SMTL ID : 4ivr.1

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x N50: 2-[(2,6-dimethoxy-5-methylpyrimidin-4-yl)methylidene]propane-1,3-diol(Non-covalent)

N50.1: 11 residues within 4Å: Chain A: H.13, E.38, W.43, I.52, I.55, Y.56, Q.80, M.83, R.118, A.123, Y.127 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.43, A:Y.127, A:Y.127 Hydrogen bonds: A:E.38, A:Y.56, A:Y.56, A:R.118 pi-Stacking: A:Y.127 N50.3: 13 residues within 4Å: Chain B: H.13, W.43, I.52, I.55, Y.56, Q.80, M.83, Y.87, R.118, A.122, A.123, Y.127, R.177 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.87 Hydrogen bonds: B:Q.80, B:R.118 Water bridges: B:H.13, B:K.17, B:R.131, B:R.177 pi-Stacking: B:Y.127

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

SO4.2: 6 residues within 4Å: Chain A: H.13, G.14, M.15, G.16, K.17, T.18 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, A:R.171 Salt bridges: A:K.17 SO4.4: 8 residues within 4Å: Chain B: H.13, G.14, M.15, G.16, K.17, T.18, R.175, R.177 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.14, B:M.15, B:G.16, B:K.17, B:T.18 Water bridges: B:K.17, B:D.117 Salt bridges: B:R.175, B:R.177

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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