SMTL ID : 4q1f.1

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 12R {N-{2-[5-(4-{(1R)-1-[(4,6-diaminopyrimidin-2-yl)sulfanyl]ethyl}-5-methyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide}

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 12 residues within 4Å: Chain A: N.49, A.51, A.52, G.53, K.54, S.55, T.56, R.208, R.212, D.261, F.262, K.263 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.56, 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:D.261, A:F.262, A:K.263 Water bridges: A:K.54, A:K.54, A:D.261, A:D.261 Salt bridges: A:K.54, A:R.212, A:R.212 pi-Cation interactions: A:R.208 UDP.3: 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 21 PLIP interactions: 21 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:E.147, B:D.261, B:F.262, B:K.263, B:K.263, B:K.263 Water bridges: B:K.54, B:R.212, B:R.212 Salt bridges: B:K.54, B:R.212, B:R.212

2 x 2XN: N-{2-[5-(4-{(1R)-1-[(4,6-diaminopyrimidin-2-yl)sulfanyl]ethyl}-5-methyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethyl}methanesulfonamide(Non-covalent)

2XN.2: 18 residues within 4Å: Chain A: I.50, E.73, V.75, L.102, M.105, Y.106, P.109, F.116, Q.117, R.124, R.148, D.153, F.157, N.160, L.161, S.164, Y.224, K.227 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.50, A:V.75, A:L.102, A:Y.106, A:F.157, A:Y.224 Hydrogen bonds: A:E.73, A:Q.117, A:R.148, A:D.153, A:N.160, A:S.164, A:K.227 pi-Stacking: A:F.157 2XN.4: 14 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, S.164, P.221, Y.224 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.102, B:P.109, B:F.157 Hydrogen bonds: B:E.73, B:Q.117, B:Q.117, B:D.153, B:Y.224 Water bridges: B:C.121 pi-Stacking: B:F.157

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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