SMTL ID : 6dmg.1

A multiconformer ligand model of EK6 bound to ERK2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: Y.177, R.181, R.184, Y.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.223 Water bridges: A:R.184 Salt bridges: A:R.181, A:R.184 SO4.2: 2 residues within 4Å: Chain A: K.197, E.293 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.197, A:K.197 Salt bridges: A:K.197 SO4.3: 2 residues within 4Å: Chain A: R.181, K.221 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.181, A:W.182 Salt bridges: A:R.181

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

EDO.4: 7 residues within 4Å: Chain A: Y.103, K.141, S.143, T.180, W.182, Y.183 Ligands: EK6.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.141 Water bridges: A:Y.183 EDO.5: 4 residues within 4Å: Chain A: D.114, H.115, Y.118, Y.306 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: L.106, K.107, T.108, Q.109, H.110, N.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.107

1 x EK6: ethyl N-{2-chloro-4-[5-(5-{[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]carbamoyl}-1H-pyrrol-3-yl)-1H-pyrazol-4-yl]benzyl}glycinate(Non-covalent)

EK6.7: 24 residues within 4Å: Chain A: I.21, G.22, E.23, G.24, A.25, Y.26, G.27, M.28, V.29, A.42, K.44, I.74, Q.95, D.96, L.97, M.98, D.101, Y.103, S.143, N.144, L.146, C.156, D.157 Ligands: EDO.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.21, A:V.29, A:K.44, A:Y.103, A:L.146 Hydrogen bonds: A:K.44, A:Q.95, A:D.96, A:M.98, A:N.144 Water bridges: A:Q.95 pi-Cation interactions: A:K.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Zundert, G.C.P. et al., qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. (2018)

Release Date

2018-12-19

Peptides

Mitogen-activated protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 1