SMTL ID : 4q1e.1

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 10 {2-{[(1R/S)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol 4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine}

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x 2Y8: (R)-2-((1-(2-(3-(2-fluoroethoxy)-4-methoxyphenyl)-5-methylthiazol-4-yl)ethyl)thio)pyrimidine-4,6-diamine(Non-covalent)

2Y8.1: 18 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, N.160, L.161, S.164, S.166, Y.224 Ligands: 2Y7.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.75, A:L.102, A:Y.106, A:F.157 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:R.148, A:S.166 Water bridges: A:C.121 pi-Stacking: A:F.157 Halogen bonds: A:N.160, A:N.160 2Y8.4: 14 residues within 4Å: Chain B: E.73, V.75, L.102, Y.106, P.109, F.116, Q.117, R.148, D.153, F.157, S.164, S.166, Y.224 Ligands: 2Y7.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.75, B:L.102, B:Y.106, B:F.116, B:F.157, B:Y.224 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:R.148, B:D.153, B:Y.224 Water bridges: B:R.148 pi-Stacking: B:F.157

2 x 2Y7: (S)-2-((1-(2-(3-(2-fluoroethoxy)-4-methoxyphenyl)-5-methylthiazol-4-yl)ethyl)thio)pyrimidine-4,6-diamine(Non-covalent)

2Y7.2: 12 residues within 4Å: Chain A: I.50, S.79, L.102, Y.106, R.214, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 2Y8.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.106, A:E.217, A:Y.224, A:Y.224 Hydrogen bonds: A:E.217, A:E.217 2Y7.5: 11 residues within 4Å: Chain B: I.50, S.79, L.102, Y.106, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 2Y8.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.50, B:L.102, B:E.216, B:E.217, B:I.220 Hydrogen bonds: B:R.214, B:E.217 Water bridges: B:Q.103 pi-Stacking: B:Y.224

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 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.262 Hydrogen bonds: A:A.51, A:G.53, A:K.54, A:S.55, A:T.56, A:R.208, A:D.261, A:D.261, A:F.262, A:K.263, A:K.263, A:K.263 Water bridges: A:K.54, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 UDP.6: 13 residues within 4Å: Chain B: N.49, A.51, A.52, G.53, K.54, S.55, T.56, E.147, R.208, R.212, D.261, F.262, K.263 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.56 Hydrogen bonds: B:A.51, B:G.53, B:K.54, B:S.55, B:T.56, B:T.56, B:T.56, B:E.147, B:R.212, B:D.261, B:F.262, B:K.263 Water bridges: B:K.54, B:K.54 Salt bridges: B:K.54 pi-Stacking: B:F.262 pi-Cation interactions: B:R.208

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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