SMTL ID : 4jlk.1

Human dCK C4S-S74E mutant in complex with UDP and the F2.2.1 inhibitoR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 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 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:D.261, A:F.262, A:K.263 Water bridges: A:K.54, A:K.54, A:R.212 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Stacking: A:F.262 pi-Cation interactions: A:R.208 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, R.212, E.260, D.261, F.262, K.263 15 PLIP interactions: 15 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:D.261, B:D.261, B:F.262 Water bridges: B:K.54, B:R.148 Salt bridges: B:K.54, B:R.212, B:R.212

4 x 1NO: 2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine(Non-covalent)

1NO.2: 16 residues within 4Å: Chain A: E.73, V.75, L.102, Y.106, P.109, F.116, Q.117, A.120, R.148, D.153, F.157, N.160, L.161, S.164, Y.224 Ligands: 1NO.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.75, A:V.75, A:L.102, A:F.116 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:D.153, A:Y.224 Water bridges: A:C.121 pi-Stacking: A:F.157 Halogen bonds: A:N.160 1NO.3: 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: 1NO.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.216, A:Y.224 Hydrogen bonds: A:R.214, A:E.217 pi-Stacking: A:Y.224 1NO.5: 15 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, L.161, S.164, S.166, Y.224 Ligands: 1NO.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: 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 1NO.6: 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: 1NO.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.50, B:Y.106, B:E.216 Hydrogen bonds: B:E.217, B:E.217 pi-Stacking: B:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, J.M. et al., Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography. J.Med.Chem. (2013)

Release Date

2013-09-18

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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