SMTL ID : 5mql.2 (1 other biounit)

Crystal structure of dCK mutant C3S in complex with masitinib and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: S.64, E.156, R.221, R.223 Ligands: UDP.2, DCM.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:S.64, A:E.156, DCM.3

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 16 residues within 4Å: Chain A: N.58, A.60, A.61, G.62, K.63, S.64, T.65, E.156, R.217, L.220, R.221, D.270, F.271, K.272 Ligands: MG.1, DCM.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.271 Hydrogen bonds: A:A.60, A:G.62, A:K.63, A:S.64, A:T.65, A:T.65, A:E.156, A:D.270, A:D.270, A:F.271, A:K.272 Salt bridges: A:K.63, A:R.221, A:R.221 pi-Cation interactions: A:R.217 UDP.4: 15 residues within 4Å: Chain B: N.58, I.59, A.60, A.61, G.62, K.63, S.64, T.65, E.156, R.217, L.220, R.221, D.270, F.271, K.272 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.271 Hydrogen bonds: B:A.60, B:A.61, B:G.62, B:K.63, B:S.64, B:S.64, B:T.65, B:T.65, B:T.65, B:D.270, B:F.271, B:K.272 Water bridges: B:K.63, B:R.157 Salt bridges: B:K.63, B:R.221, B:R.221 pi-Cation interactions: B:R.217

1 x DCM: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DCM.3: 19 residues within 4Å: Chain A: I.59, A.60, K.63, E.82, W.87, L.111, Y.115, F.125, Q.126, A.129, E.156, R.157, D.162, F.166, R.221, R.223, E.226 Ligands: MG.1, UDP.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.59, A:W.87 Hydrogen bonds: A:A.60, A:E.82, A:Y.115, A:Y.115, A:Q.126, A:E.156, A:D.162, A:D.162, A:E.226, A:Y.233 Salt bridges: A:K.63, A:R.157, A:R.221, A:R.223 pi-Stacking: A:F.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hammam, K. et al., Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology. Nat Commun (2017)

Release Date

2017-11-22

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Deoxycytidine kinase

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