SMTL ID : 2zi9.1

C4S-E247A dCK variant of dCK in complex with cladribine+ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: I.49, A.50, A.51, G.52, K.53, S.54, T.55, R.207, R.211, E.259, D.260, F.261 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.50, A:G.52, A:K.53, A:S.54, A:T.55, A:T.55, A:R.207, A:E.259, A:F.261 Water bridges: A:F.56, A:R.213, A:R.213 Salt bridges: A:K.53, A:R.211, A:R.211 pi-Cation interactions: A:R.207 ADP.3: 14 residues within 4Å: Chain B: N.48, A.50, A.51, G.52, K.53, S.54, T.55, R.207, L.210, R.211, D.260, F.261, Y.265 Ligands: CL9.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.48, B:A.50, B:G.52, B:K.53, B:S.54, B:T.55, B:T.55, B:R.207, B:E.259, B:F.261 Salt bridges: B:K.53, B:R.211, B:R.211 pi-Stacking: B:F.261 pi-Cation interactions: B:R.207

2 x CL9: 2-chloro-2'-deoxyadenosine(Non-covalent)

CL9.2: 15 residues within 4Å: Chain A: I.49, E.72, W.77, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, L.160, R.213, E.216, Y.223 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.49 Hydrogen bonds: A:E.72, A:Y.105, A:Y.105, A:Q.116, A:Q.116, A:R.123, A:R.147, A:R.147, A:D.152 pi-Stacking: A:F.115, A:F.156, A:F.156 CL9.4: 15 residues within 4Å: Chain B: I.49, E.72, W.77, M.104, Y.105, F.115, Q.116, R.123, R.147, D.152, F.156, R.211, E.216, Y.223 Ligands: ADP.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.49 Hydrogen bonds: B:Y.105, B:Q.116, B:R.123, B:R.147, B:D.152, B:D.152 Water bridges: B:R.213 pi-Stacking: B:F.115, B:F.156, B:F.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabini, E. et al., Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase. J.Med.Chem. (2008)

Release Date

2008-07-08

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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