SMTL ID : 5byz.1

ERK5 in complex with small molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x 4WE: 4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl)ethyl]benzamide(Non-covalent)

4WE.1: 17 residues within 4Å: Chain A: I.14, G.15, Y.19, V.22, A.35, K.37, I.68, L.90, D.91, M.93, E.94, D.96, H.98, Q.99, S.139, L.142, D.153 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.19, A:Y.19, A:H.98, A:L.142, A:D.153 Hydrogen bonds: A:K.37, A:M.93, A:M.93, A:Q.99 Water bridges: A:Q.99 Salt bridges: A:D.96

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.137, P.138, S.139, T.177 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.98, A:K.137, A:S.139 Water bridges: A:Y.180, A:E.207 GOL.3: 4 residues within 4Å: Chain A: P.106, L.107, T.108, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.107, A:R.211 GOL.4: 1 residues within 4Å: Chain A: E.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.145 Water bridges: A:E.145 GOL.5: 4 residues within 4Å: Chain A: Q.213, L.214, V.230, V.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.214 Water bridges: A:R.212 GOL.6: 3 residues within 4Å: Chain A: I.101, H.102, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.101, A:H.102 GOL.7: 4 residues within 4Å: Chain A: H.61, Y.125, C.312, A.313 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.61, A:H.61, A:Y.125 Water bridges: A:D.311, A:D.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, H. et al., Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-05-04

Peptides

Mitogen-activated protein kinase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 7