SMTL ID : 5mql.1 (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

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

UDP.1: 12 residues within 4Å: Chain A: A.60, A.61, G.62, K.63, S.64, T.65, E.156, R.217, R.221, D.270, F.271, K.272 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.271 Hydrogen bonds: A:A.60, A:A.61, A:G.62, A:K.63, A:S.64, A:T.65, A:T.65, A:D.270, A:D.270, A:F.271, A:K.272, A:K.272, A:K.272 Salt bridges: A:K.63, A:R.221, A:R.221 UDP.3: 15 residues within 4Å: Chain B: 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: DCM.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.65, B:F.271 Hydrogen bonds: B:A.60, B:A.61, B:G.62, B:K.63, B:S.64, B:T.65, B:T.65, B:T.65, B:D.270, B:F.271, B:K.272 Water bridges: B:R.217 Salt bridges: B:K.63, B:R.221, B:R.221 pi-Cation interactions: B:R.217

1 x G65: Masitinib(Non-covalent)

G65.2: 16 residues within 4Å: Chain A: E.82, V.84, L.111, M.114, Y.115, P.118, E.119, F.125, Q.126, R.157, D.162, F.166, S.173, E.174, C.175, Y.233 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.84, A:L.111, A:Y.115, A:Y.115, A:P.118 Hydrogen bonds: A:Q.126 Salt bridges: A:E.119, A:E.119 pi-Stacking: A:F.166

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

DCM.4: 18 residues within 4Å: Chain B: I.59, K.63, E.82, V.84, W.87, L.111, M.114, Y.115, F.125, Q.126, E.156, R.157, D.162, F.166, R.221, R.223, E.226 Ligands: UDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.59 Hydrogen bonds: B:Y.115, B:Y.115, B:Q.126, B:E.156, B:D.162, B:E.226 Salt bridges: B:K.63, B:R.157, B:R.221, B:R.223 pi-Stacking: B: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
A

B
B

Deoxycytidine kinase

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