SMTL ID : 7w5o.1 (1 other biounit)

Crystal structure of ERK2 with an allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: 14 residues within 4Å: Chain A: I.39, G.40, V.47, A.60, Q.113, D.114, L.115, M.116, D.119, K.122, S.161, N.162, L.164 Ligands: NA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.114, A:M.116, A:D.119, A:K.122, A:K.122, A:S.161 Halogen bonds: A:Q.113

3 x MLA: MALONIC ACID(Non-covalent)

MLA.2: 5 residues within 4Å: Chain A: L.129, L.230, F.287, N.289, A.290 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.230 Hydrogen bonds: A:L.230, A:N.289, A:N.289 MLA.6: 6 residues within 4Å: Chain A: F.191, E.194, Y.195, V.196, R.202, I.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.194, A:V.196 Salt bridges: A:R.202 MLA.7: 5 residues within 4Å: Chain A: Y.121, K.159, P.160, S.161, Y.201 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.121 Hydrogen bonds: A:S.161 Salt bridges: A:K.159, A:K.159

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 10 residues within 4Å: Chain A: G.42, A.43, Y.44, K.62, I.64, R.75, E.79, D.175, G.177 Ligands: NA.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.44, A:I.64 Hydrogen bonds: A:A.43, A:Y.44, A:Y.44, A:D.175, A:G.177 Water bridges: A:Y.44, A:Y.44 Salt bridges: A:K.62, A:K.62 SIN.5: 6 residues within 4Å: Chain A: K.300, K.308, R.309, I.310, E.311, Q.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.309, A:Q.314 Salt bridges: A:K.300

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: K.62, C.174, D.175 Ligands: 5ID.1, SIN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62, A:K.62 Water bridges: A:D.175

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 12 residues within 4Å: Chain A: Q.70, T.71, Q.74, R.75, R.156, L.178, R.180, T.193, E.194, Y.195, D.344, D.345 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.74, A:R.156, A:Y.195 Water bridges: A:R.180, A:R.180 Salt bridges: A:R.75, A:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, M. et al., Identification of a novel target site for ATP-independent ERK2 inhibitors. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-02-23

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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