SMTL ID : 2a7q.1

Crystal structure of human dCK complexed with clofarabine and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.38, E.56, E.130 Ligands: ADP.2, CFB.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.130 MG.4: 5 residues within 4Å: Chain B: S.38, E.56, E.130 Ligands: ADP.5, CFB.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.130

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

ADP.2: 13 residues within 4Å: Chain A: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, V.241, E.243, D.244, F.245 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.34, A:A.35, A:G.36, A:K.37, A:S.38, A:T.39, A:T.39, A:E.243, A:F.245 Water bridges: A:K.37, A:R.131, A:R.191, A:R.191, A:R.197, A:R.197 Salt bridges: A:K.37 pi-Cation interactions: A:R.191, A:R.191 ADP.5: 13 residues within 4Å: Chain B: N.32, A.34, A.35, G.36, K.37, S.38, T.39, R.191, V.241, E.243, D.244, F.245 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.34, B:A.35, B:G.36, B:K.37, B:S.38, B:T.39, B:T.39, B:E.243, B:F.245 Water bridges: B:K.37, B:R.131, B:R.191, B:R.191, B:R.197, B:R.197 Salt bridges: B:K.37 pi-Cation interactions: B:R.191, B:R.191

2 x CFB: 2-CHLORO-9-(2-DEOXY-2-FLUORO-B -D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE(Non-covalent)

CFB.3: 17 residues within 4Å: Chain A: I.33, E.56, V.58, W.61, M.88, Y.89, F.99, Q.100, R.107, R.131, D.136, F.140, L.144, R.197, E.200, Y.207 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.100, A:R.107, A:R.131, A:D.136, A:E.200 Water bridges: A:R.131 pi-Stacking: A:F.99, A:F.140, A:F.140 Halogen bonds: A:R.131 CFB.6: 17 residues within 4Å: Chain B: I.33, E.56, V.58, W.61, M.88, Y.89, F.99, Q.100, R.107, R.131, D.136, F.140, L.144, R.197, E.200, Y.207 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.89, B:Q.100, B:R.107, B:R.131, B:D.136, B:D.136, B:E.200, B:E.200 Water bridges: B:R.131 pi-Stacking: B:F.99, B:F.140, B:F.140 Halogen bonds: B:R.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., The structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-01-24

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidine kinase

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