SMTL ID : 4qtb.1 (1 other biounit)

Structure of human ERK1 in complex with SCH772984 revealing a novel inhibitor-induced binding pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.38, L.108, R.109, Y.120 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.38, A:G.40 EDO.2: 5 residues within 4Å: Chain A: E.99, N.100, Q.150, R.153, D.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.100, A:N.100, A:R.153, A:D.180 Water bridges: A:R.153, A:L.181 EDO.3: 3 residues within 4Å: Chain A: L.202, E.204, Y.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.202, A:E.204 Water bridges: A:Y.251 EDO.4: 7 residues within 4Å: Chain A: Q.84, R.85, R.88, G.187, L.188, A.189, R.190 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.84, A:R.88, A:R.190 Water bridges: A:Q.84, A:R.190 EDO.5: 3 residues within 4Å: Chain A: Y.131, S.171 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.171, A:S.171 EDO.6: 6 residues within 4Å: Chain A: I.191, A.192, D.193, T.348, F.349 Ligands: DMS.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.192, A:F.349, A:F.349 EDO.7: 3 residues within 4Å: Chain A: D.142, Y.146, Y.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.334 Water bridges: A:D.142 EDO.8: 6 residues within 4Å: Chain A: L.259, S.264, L.285, P.286, K.288 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: S.264, L.282, Q.283, L.285, S.287 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.283 EDO.10: 4 residues within 4Å: Chain A: E.323, E.324, A.327, Y.335 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.335, A:Y.335 EDO.11: 4 residues within 4Å: Chain A: P.41, R.42, H.63, V.64 No protein-ligand interaction detected (PLIP) EDO.12: 1 residues within 4Å: Chain A: K.66 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.66, A:K.66 EDO.13: 4 residues within 4Å: Chain A: D.129, Y.131, K.132 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.129 Water bridges: A:K.132

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 4 residues within 4Å: Chain A: I.144, L.240, K.299, S.300 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.301 DMS.15: 7 residues within 4Å: Chain A: R.190, I.191, D.193, Y.223, F.349, M.351 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.191 Water bridges: A:R.190 Salt bridges: A:D.193 pi-Cation interactions: A:Y.223

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

CL.16: 5 residues within 4Å: Chain A: H.198, N.219, I.273, I.274, N.275 Ligand excluded by PLIP

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

SO4.17: 4 residues within 4Å: Chain A: Y.205, R.209, R.212, Y.251 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.209, A:R.212, A:Y.251, A:Y.251 Salt bridges: A:R.209, A:R.212

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.18: 22 residues within 4Å: Chain A: I.49, A.53, Y.54, A.70, K.72, I.74, Y.82, R.85, T.86, E.89, Q.123, D.124, L.125, M.126, E.127, T.128, D.129, K.132, L.174, C.184, D.185, G.187 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.54, A:Y.54, A:A.70, A:K.72, A:Y.82, A:Y.82, A:Q.123, A:L.174 Hydrogen bonds: A:K.72, A:M.126, A:M.126, A:K.132 Water bridges: A:D.185 Salt bridges: A:E.89, A:D.185 pi-Stacking: A:Y.82

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 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 3

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