SMTL ID : 8aoj.1

Specific covalent inhibitor of ERK2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Y.195, R.199, R.202, H.240, Y.241 8 PLIP interactions: 8 interactions with chain A Water bridges: A:Y.195, A:R.199, A:R.199, A:R.202, A:Y.241, A:Y.241 Salt bridges: A:R.199, A:R.202 SO4.6: 5 residues within 4Å: Chain A: R.75, R.156, R.180, V.196, Y.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.213 Water bridges: A:R.156, A:R.180 Salt bridges: A:R.75, A:R.156, A:R.180

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

EDO.2: 1 residues within 4Å: Chain A: I.264 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: L.124, K.125, H.128, N.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.125 Water bridges: A:H.128, A:S.231 EDO.4: 3 residues within 4Å: Chain A: E.194, Y.241, L.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.194 Water bridges: A:L.242

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

DMS.5: 5 residues within 4Å: Chain A: D.28, I.98, R.99, A.100, Y.110 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.28

1 x N8L: 1-[(2~{S})-2-(5-methyl-3-pyridin-4-yl-1~{H}-pyrazol-4-yl)pyrrolidin-1-yl]propan-1-one(Covalent)

N8L.7: 17 residues within 4Å: Chain A: I.39, V.47, A.60, K.62, Q.113, D.114, L.115, M.116, E.117, T.118, D.119, K.122, S.161, N.162, L.164, C.174, D.175 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.47, A:A.60, A:L.115, A:L.164, A:D.175 Hydrogen bonds: A:D.114, A:M.116, A:K.122 Water bridges: A:K.62, A:K.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St Denis, J.D. et al., X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor. J.Med.Chem. (2022)

Release Date

2022-09-28

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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