SMTL ID : 4jlm.1

Human dCK C4S-S74E mutant in complex with UDP and the F2.3.1 inhibitor (2-[({5-ETHYL-2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

3 x 1NN: 2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine(Non-covalent)(Covalent)

1NN.1: 16 residues within 4Å: Chain A: E.73, V.75, L.102, M.105, Y.106, P.109, Q.117, A.120, R.148, D.153, F.157, N.160, L.161, S.164, Y.224 Ligands: 1NN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.75, A:L.102, A:Y.106 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:R.148, A:D.153, A:Y.224 pi-Stacking: A:F.157 Halogen bonds: A:N.160 1NN.2: 11 residues within 4Å: Chain A: I.50, L.102, Y.106, R.214, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 1NN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.50, A:I.220, A:I.220, A:Y.224, A:Y.224 Hydrogen bonds: A:Y.106, A:R.214, A:E.217 1NN.4: 13 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.75, B:V.75, B:L.102, B:Y.106 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:R.148 pi-Stacking: B:F.157

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, E.147, R.208, R.212, D.261, F.262, K.263 21 PLIP interactions: 21 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:T.56, A:T.56, A:E.147, A:D.261, A:F.262, A:K.263 Water bridges: A:K.54, A:K.54, A:S.55, A:R.212, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 UDP.5: 15 residues within 4Å: Chain B: N.49, I.50, 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 22 PLIP interactions: 22 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:T.56, B:D.261, B:F.262, B:K.263, B:K.263, B:K.263 Water bridges: B:E.147, B:R.148, B:R.212, B:E.217 Salt bridges: B:K.54, B:R.212, B:R.212 pi-Cation interactions: B:K.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomme, J. et al., Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-01-22

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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