SMTL ID : 4q1c.1

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 8 {2,2'-[{4-[(2R)-4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-2,3-dihydro-1,3-thiazol-2-yl]benzene-1,2-diyl}bis(oxy)]diethanol}

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 2XM: 2,2'-((4-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)-1,2-phenylene)bis(oxy))bis(ethan-1-ol)(Non-covalent)

2XM.1: 14 residues within 4Å: Chain A: 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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.75, A:V.75, A:L.102, A:Y.106, A:Y.224 Hydrogen bonds: A:E.73, A:Q.117, A:Q.117, A:R.148, A:D.153, A:S.164, A:S.164, A:S.166, A:Y.224 Water bridges: A:C.121 pi-Stacking: A:Y.106, A:F.157 2XM.3: 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, L.161, S.164, Y.224 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.75, B:Y.106, B:Y.106, B:F.116, B:Y.224 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:S.164, B:S.164 Water bridges: B:E.73 pi-Stacking: B:F.116, B:F.157

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

UDP.2: 14 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, E.260, D.261, F.262, K.263 17 PLIP interactions: 17 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.208 Salt bridges: A:K.54, A:R.212, A:R.212 UDP.4: 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: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.212, B:R.212, B:R.214 Salt bridges: B:K.54, B:R.212, B:R.212 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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