SMTL ID : 2j90.1

Crystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x IZA: 2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE(Non-covalent)

IZA.1: 14 residues within 4Å: Chain A: L.34, S.36, V.42, A.55, K.57, I.92, L.108, E.109, L.110, V.111, M.161, I.175, D.176 Ligands: CL.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.34, A:L.34, A:V.42, A:V.111, A:I.175, A:D.176 Hydrogen bonds: A:E.109, A:V.111 IZA.4: 15 residues within 4Å: Chain B: L.34, S.36, V.42, A.55, K.57, I.92, L.108, E.109, L.110, V.111, N.159, M.161, I.175, D.176 Ligands: CL.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.34, B:L.34, B:V.42, B:L.108, B:V.111, B:I.175, B:D.176 Hydrogen bonds: B:E.109, B:V.111

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: K.57, D.176 Ligands: IZA.1 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: K.57, D.176 Ligands: IZA.4 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.57, I.59, E.79, G.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.57, A:E.79 Water bridges: A:D.176 EDO.6: 3 residues within 4Å: Chain B: K.276, R.278, Q.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.283 EDO.7: 5 residues within 4Å: Chain B: A.40, K.57, I.59, V.71, E.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.57, B:K.57 Water bridges: B:E.79

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain A: Y.144, K.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.144 Water bridges: A:K.148 Salt bridges: A:K.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pike, A.C.W. et al., Activation Segment Dimerization: A Mechanism for Kinase Autophosphorylation of Non-Consensus Sites. Embo J. (2008)

Release Date

2006-11-07

Peptides

DEATH-ASSOCIATED PROTEIN KINASE 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DEATH-ASSOCIATED PROTEIN KINASE 3