SMTL ID : 7zi1.1

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the dCKi1 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:A.51, A:A.52, A:G.53, A:K.54, A:S.55, A:T.56, A:T.56, A:T.56, A:E.147, A:D.261, A:F.262, A:K.263, A:K.263, A:K.263 Water bridges: A:K.54, A:K.54, A:R.214, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Stacking: A:F.262 pi-Cation interactions: A:R.208, A:K.263 UDP.5: 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 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:T.56, B:D.261, B:F.262, B:K.263, B:K.263, B:K.263 Water bridges: B:K.54, B:K.54, B:R.214, B:R.214 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Stacking: B:F.262 pi-Cation interactions: B:R.208, B:K.263

4 x JCA: N-[3-[[4-(4-azanylpyrimidin-2-yl)-1,3-thiazol-2-yl]amino]-4-methyl-phenyl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide(Non-covalent)

JCA.2: 17 residues within 4Å: Chain A: E.73, V.75, L.102, M.105, Y.106, P.109, E.110, F.116, Q.117, R.148, D.153, F.157, L.161, S.164, E.165, S.166 Ligands: JCA.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.75, A:L.102, A:M.105, A:Y.106, A:Y.106, A:P.109 Hydrogen bonds: A:Q.117, A:Q.117, A:D.153 Water bridges: A:R.148 Salt bridges: A:E.110 pi-Stacking: A:F.116, A:F.157 JCA.3: 9 residues within 4Å: Chain A: I.50, Y.106, S.164, E.165, I.220, P.221, Y.224, K.227 Ligands: JCA.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.220 Hydrogen bonds: A:Y.224, A:Y.224 JCA.6: 17 residues within 4Å: Chain B: E.73, V.75, L.102, M.105, Y.106, P.109, E.110, F.116, Q.117, R.148, D.153, F.157, L.161, S.164, E.165, S.166 Ligands: JCA.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.75, B:L.102, B:M.105, B:Y.106, B:Y.106, B:P.109 Hydrogen bonds: B:Q.117, B:Q.117 Water bridges: B:R.148, B:Y.224 Salt bridges: B:E.110 pi-Stacking: B:F.116, B:F.157 JCA.7: 9 residues within 4Å: Chain B: I.50, Y.106, S.164, E.165, I.220, P.221, Y.224, K.227 Ligands: JCA.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.220 Hydrogen bonds: B:Y.224

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: K.62, S.65, E.66, W.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.68 NA.8: 4 residues within 4Å: Chain B: K.62, S.65, E.66, W.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saez-Ayala, M. et al., From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia. Nat Commun (2023)

Release Date

2023-06-07

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Deoxycytidine kinase

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