SMTL ID : 4q18.1

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 4 [1-[5-(4-{[(2,6-diaminopyrimidin-4-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x 2XJ: 1-(5-(4-(((2,6-diaminopyrimidin-4-yl)thio)methyl)-5-propylthiazol-2-yl)-2-methoxyphenoxy)-2-methylpropan-2-ol(Non-covalent)

2XJ.1: 17 residues within 4Å: Chain A: E.73, V.75, L.102, M.105, Y.106, P.109, F.116, Q.117, A.120, R.148, D.153, F.157, L.161, S.164, S.166, Y.224 Ligands: 2XJ.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.75, A:F.116 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:R.148, A:S.164, A:S.164, A:S.166 Water bridges: A:R.124, A:R.124 Salt bridges: A:D.153 pi-Stacking: A:F.157 2XJ.2: 10 residues within 4Å: Chain A: I.50, S.79, Y.106, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 2XJ.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.50, A:Y.106, A:E.216, A:I.220, A:Y.224, A:Y.224, A:Y.224 Hydrogen bonds: A:S.79, A:E.216 Salt bridges: A:E.217 2XJ.5: 17 residues within 4Å: Chain B: E.73, V.75, L.102, M.105, P.109, F.116, Q.117, R.148, D.153, F.157, N.160, L.161, S.164, S.166, Y.224, K.227 Ligands: 2XJ.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.102, B:M.105, B:P.109, B:F.116, B:L.161 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:S.164, B:S.164, B:S.166 Water bridges: B:R.124, B:R.124 Salt bridges: B:D.153 pi-Stacking: B:F.157 2XJ.6: 12 residues within 4Å: Chain B: I.50, S.79, L.102, Y.106, R.214, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 2XJ.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.50, B:Y.106, B:E.217, B:I.220, B:Y.224 Hydrogen bonds: B:R.214, B:R.214, B:E.217 Salt bridges: B:E.216

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

UDP.3: 13 residues within 4Å: Chain A: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, L.211, R.212, D.261, F.262, K.263 18 PLIP interactions: 18 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:R.208, A:D.261, A:F.262, A:K.263, A:K.263 Water bridges: A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Stacking: A:F.262 UDP.4: 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 Hydrogen bonds: B:A.51, B:A.52, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:D.261, B:D.261, B:F.262, B:K.263 Water bridges: B:K.54, B:K.54 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomme, J. et al., Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability. J.Med.Chem. (2014)

Release Date

2014-11-05

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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