SMTL ID : 3ipx.2 (1 other biounit)

X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: N.10, A.12, A.13, G.14, K.15, S.16, T.17, E.108, R.169, L.172, R.173, V.219, E.221, D.222, F.223 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.12, A:A.13, A:G.14, A:K.15, A:S.16, A:T.17, A:T.17, A:E.108, A:E.221, A:F.223 Water bridges: A:K.15, A:K.15, A:S.16, A:T.17, A:R.169, A:R.169, A:R.169, A:R.175 Salt bridges: A:K.15 pi-Cation interactions: A:R.169, A:R.169 ADP.4: 16 residues within 4Å: Chain B: N.10, A.12, A.13, G.14, K.15, S.16, T.17, E.108, R.169, L.172, R.173, V.219, E.221, D.222, F.223 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:A.12, B:A.13, B:G.14, B:K.15, B:S.16, B:T.17, B:T.17, B:E.108, B:R.169, B:E.221, B:F.223 Water bridges: B:K.15, B:K.15, B:S.16, B:T.17, B:R.169, B:R.169, B:R.175 Salt bridges: B:K.15 pi-Cation interactions: B:R.169, B:R.169

2 x B86: 2'-deoxy-5-fluorocytidine(Non-covalent)

B86.2: 14 residues within 4Å: Chain A: I.11, E.34, V.36, W.39, L.63, M.66, Y.67, F.77, Q.78, R.85, R.109, D.114, F.118, E.178 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.11, A:F.118 Hydrogen bonds: A:E.34, A:Q.78, A:R.109, A:D.114, A:E.178 Water bridges: A:R.109 pi-Stacking: A:F.118 B86.5: 14 residues within 4Å: Chain B: I.11, E.34, V.36, W.39, L.63, M.66, Y.67, F.77, Q.78, R.85, R.109, D.114, F.118, E.178 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.11, B:F.118 Hydrogen bonds: B:E.34, B:Y.67, B:Q.78, B:R.109, B:D.114, B:D.114, B:E.178, B:E.178 Water bridges: B:R.109 pi-Stacking: B:F.118

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.16, E.108 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.16, A:E.108, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: S.16, E.108 Ligands: ADP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.16, B:E.108, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jessop, T.C. et al., Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors. Bioorg.Med.Chem.Lett. (2009)

Release Date

2010-08-18

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidine kinase

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