SMTL ID : 7x4u.1

Crystal structure of ERK2 with an allosteric inhibitor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x 5ID: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL(Non-covalent)

5ID.1: 15 residues within 4Å: Chain A: I.39, E.41, V.47, A.60, I.92, Q.113, D.114, L.115, M.116, E.117, T.118, D.119, K.122, S.161, L.164 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.164 Hydrogen bonds: A:D.114, A:M.116, A:D.119, A:D.119, A:K.122 Water bridges: A:D.119, A:D.119 Halogen bonds: A:Q.113

1 x 8DK: N-(1,3-benzodioxol-5-ylmethyl)-2-[3-(3,4-dimethylphenyl)-7-oxidanylidene-[1,2,3]triazolo[4,5-d]pyrimidin-6-yl]ethanamide(Non-covalent)

8DK.2: 6 residues within 4Å: Chain A: Q.127, D.132, H.133, Y.136, T.168, Y.324 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:H.133, A:H.133, A:Y.136

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: P.288, N.289, A.290, D.291, S.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.290, A:S.292 Water bridges: A:A.290 GOL.5: 6 residues within 4Å: Chain A: L.124, K.125, T.126, Q.127, H.128, N.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.128, A:N.232 GOL.6: 6 residues within 4Å: Chain A: L.129, I.134, M.229, L.230, N.289, A.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.230, A:L.230 Water bridges: A:A.290

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 5 residues within 4Å: Chain A: E.322, Q.323, Y.324, Y.325, D.326 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.324

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

SO4.7: 3 residues within 4Å: Chain A: F.191, L.242, Y.271 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kinoshita, T. et al., Structural basis for producing allosteric ERK2 inhibitors. To Be Published

Release Date

2023-03-08

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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