SMTL ID : 8ooj.2 (2 other biounits)

Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 14 residues within 4Å: Chain A: N.49, A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, L.211, R.212, D.261, F.262, K.263 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.262 Hydrogen bonds: A:A.51, A:A.52, A:G.53, A:K.54, A:S.55, A:T.56, A:D.261, A:F.262, A:K.263 Water bridges: A:R.212, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208, A:K.263 UDP.3: 14 residues within 4Å: Chain B: N.49, A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, L.211, R.212, D.261, F.262, K.263 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.262 Hydrogen bonds: B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:E.147, B:D.261, B:F.262, B:K.263 Water bridges: B:R.212, B:R.214 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Cation interactions: B:R.208, B:K.263

2 x VVC: 4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one(Non-covalent)

VVC.2: 13 residues within 4Å: Chain A: I.50, E.73, V.75, L.102, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.216, E.217 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.50, A:V.75, A:L.102, A:F.157 Hydrogen bonds: A:E.73, A:Q.117, A:R.148, A:D.153, A:E.217 Water bridges: A:R.214 pi-Stacking: A:F.157 VVC.4: 13 residues within 4Å: Chain B: I.50, E.73, V.75, L.102, Y.106, F.116, Q.117, R.148, D.153, F.157, R.214, E.216, E.217 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.50, B:V.75, B:L.102, B:F.157 Hydrogen bonds: B:E.73, B:Y.106, B:Q.117, B:R.148, B:D.153, B:D.153 Water bridges: B:R.214 pi-Stacking: B:F.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calbert, M.L. et al., 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress. Mol.Cancer Ther. (2023)

Release Date

2023-12-20

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Deoxycytidine kinase

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