SMTL ID : 4qta.1

Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: R.92, A.93, Q.98, M.99, K.100, D.101 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.93, A:K.100, A:D.101, A:D.101 Water bridges: A:D.101 EDO.2: 5 residues within 4Å: Chain A: V.22, G.23, P.24, R.25, I.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.25 EDO.3: 7 residues within 4Å: Chain A: R.78, Y.140, A.144, A.326, E.327, A.328, F.330 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.78, A:E.327, A:A.328 Water bridges: A:Y.140, A:Y.140 EDO.4: 5 residues within 4Å: Chain A: R.25, N.48, N.88, D.89, F.355 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:R.25, A:N.48, A:D.89 EDO.5: 3 residues within 4Å: Chain A: G.35, A.36, Y.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.36 Water bridges: A:Y.37 EDO.6: 4 residues within 4Å: Chain A: K.139, P.320, E.323, I.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.139 EDO.7: 6 residues within 4Å: Chain A: D.21, I.91, R.92, A.93, Y.103 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.21 EDO.8: 4 residues within 4Å: Chain A: A.353, Q.356, P.357, G.358 No protein-ligand interaction detected (PLIP)

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

SO4.9: 3 residues within 4Å: Chain A: H.62, Q.63, T.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.63, A:T.64 Water bridges: A:T.64 Salt bridges: A:H.62 SO4.10: 1 residues within 4Å: Chain A: R.226 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.226

1 x 38Z: (3R)-1-(2-oxo-2-{4-[4-(pyrimidin-2-yl)phenyl]piperazin-1-yl}ethyl)-N-[3-(pyridin-4-yl)-2H-indazol-5-yl]pyrrolidine-3-carboxamide(Non-covalent)

38Z.11: 23 residues within 4Å: Chain A: I.32, A.36, Y.37, A.53, K.55, I.57, P.59, Y.65, R.68, T.69, E.72, Q.106, D.107, L.108, M.109, E.110, T.111, D.112, K.115, L.157, C.167, D.168, G.170 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.32, A:Y.37, A:A.53, A:K.55, A:I.57, A:P.59, A:Y.65, A:Y.65, A:Q.106, A:L.157 Hydrogen bonds: A:K.55, A:E.72, A:M.109, A:M.109, A:K.115 Water bridges: A:Y.65, A:Q.106 Salt bridges: A:E.72, A:D.168 pi-Stacking: A:Y.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics. Nat.Chem.Biol. (2014)

Release Date

2014-07-23

Peptides

Mitogen-activated protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 1

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