SMTL ID : 8pt3.1

ERK2 covelently bound to RU77 cyclohexenone based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x D7O: ~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{S},5~{R})-6-methylidene-4-oxidanylidene-bicyclo[3.2.1]octane-1,3-dicarboxylate(Covalent)

D7O.1: 5 residues within 4Å: Chain A: Q.123, D.128, H.129, F.133, C.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.133 Water bridges: A:S.126 Salt bridges: A:H.129, A:H.129

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: E.85, N.86, Y.132, Q.136, R.139, D.166 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.86, A:N.86, A:R.139, A:D.166, A:D.166 Water bridges: A:Y.132, A:L.167, A:K.168 GOL.3: 10 residues within 4Å: Chain A: Y.40, K.58, I.60, Y.68, R.71, T.72, E.75, D.171, G.173 Ligands: ANP.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.40, A:Y.40, A:K.58, A:R.71, A:R.71, A:G.173 GOL.4: 6 residues within 4Å: Chain A: H.303, K.304, R.305, I.306, E.307, Q.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.307, A:E.307, A:Q.310

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 20 residues within 4Å: Chain A: I.35, G.36, E.37, G.38, V.43, A.56, K.58, I.88, Q.109, D.110, L.111, M.112, D.115, K.118, K.155, S.157, N.158, L.160, D.171 Ligands: GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.109, A:M.112, A:K.118, A:K.118, A:K.155, A:S.157, A:N.158, A:N.158, A:D.171 Salt bridges: A:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poti, A.L. et al., Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold. Nat Commun (2024)

Release Date

2024-07-24

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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