SMTL ID : 4jlj.1

Human dCK C4S-S74E mutant in complex with UDP and the F2.1.1 inhibitor (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

1NM.1: 16 residues within 4Å: Chain A: E.73, V.75, L.102, M.105, Y.106, P.109, F.116, Q.117, R.148, D.153, F.157, N.160, L.161, S.164, Y.224 Ligands: 1NM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.75, A:Y.106 Hydrogen bonds: A:E.73, A:Q.117, A:R.148, A:D.153, A:D.153 Water bridges: A:R.148 pi-Stacking: A:F.157 1NM.2: 11 residues within 4Å: Chain A: S.79, L.102, Y.106, R.214, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 1NM.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.106, A:I.220, A:Y.224, A:Y.224 Hydrogen bonds: A:R.214, A:E.216, A:E.217 1NM.4: 16 residues within 4Å: Chain B: E.73, V.75, L.102, M.105, Y.106, P.109, F.116, Q.117, R.148, D.153, F.157, N.160, L.161, S.164, S.166 Ligands: 1NM.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.75 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:R.148 Water bridges: B:R.148 pi-Stacking: B:F.157 Halogen bonds: B:N.160 1NM.5: 11 residues within 4Å: Chain B: S.79, L.102, Y.106, R.214, E.216, E.217, G.219, I.220, P.221, Y.224 Ligands: 1NM.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.102, B:E.216, B:I.220, B:Y.224 Hydrogen bonds: B:S.79, B:E.217, B:E.217 Water bridges: B:R.214 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 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:R.208, A:D.261, A:F.262, A:K.263 Water bridges: A:K.54, A:R.148, A:R.212 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208, A:K.263 UDP.6: 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 Hydrophobic interactions: B:T.56 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, B:K.263, B:K.263 Water bridges: B:K.54, B:K.54, 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

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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