SMTL ID : 4q1a.1

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6 {2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol}

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 2XZ: 2-(5-(4-(((4,6-DIAMINOPYRIMIDIN-2-YL)THIO)METHYL)-5-PROPYLTHIAZOL-2-YL)-2-METHOXYPHENOXY)ETHAN-1-OL(Non-covalent)

2XZ.1: 15 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, L.161, S.164, S.166, Y.224 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.75, A:V.75, A:L.102, A:Y.106, A:F.116 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, A:R.148 pi-Stacking: A:Y.106, A:F.157 2XZ.3: 13 residues within 4Å: Chain B: I.50, E.73, V.75, M.105, Y.106, P.109, Q.117, R.148, D.153, F.157, L.161, S.164, Y.224 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.50, B:Y.106, B:Y.106, B:Y.224 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:R.148, B:S.164 pi-Stacking: B:F.157

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

UDP.2: 13 residues within 4Å: Chain A: 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 20 PLIP interactions: 20 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 Water bridges: A:K.54, A:K.54, A:R.214, A:R.214 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 UDP.4: 13 residues within 4Å: Chain B: 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 B 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 Salt bridges: B:K.54, B:R.212, B:R.212 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

2015-02-18

Peptides

Deoxycytidine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxycytidine kinase

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