SMTL ID : 7jus.1

Crystal Structure of KSR2:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor Cobimetinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

hetero-1-1-mer

Ligands

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

ANP.1: 16 residues within 4Å: Chain A: K.66, G.67, R.68, V.72, A.82, R.84, T.131, S.132, C.134, T.138, K.180, K.182, N.183, F.185, D.195 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:R.68, A:T.131, A:S.132, A:C.134, A:K.180 Water bridges: A:N.183, A:D.195 Salt bridges: A:R.84 ANP.4: 15 residues within 4Å: Chain B: L.65, V.73, A.86, K.88, M.134, E.135, M.137, S.141, Q.144, K.183, S.185, N.186, D.199 Ligands: VKD.3, MG.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.88, B:E.135, B:M.137, B:S.141, B:S.141, B:Q.144, B:K.183, B:S.185, B:N.186 Salt bridges: B:K.88

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.183, D.195 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.195, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: K.88, N.186, D.199 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.199

1 x VKD: Cobimetinib(Non-covalent)

VKD.3: 16 residues within 4Å: Chain B: K.88, L.106, L.109, V.118, I.132, M.134, D.181, K.183, N.186, D.199, F.200, V.202, S.203, L.206, I.207 Ligands: ANP.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.109, B:I.207 Hydrogen bonds: B:K.88, B:D.199, B:D.199, B:D.199 Halogen bonds: B:V.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, Z.M. et al., Structural basis for the action of the drug trametinib at KSR-bound MEK. Nature (2020)

Release Date

2020-09-30

Peptides

Kinase suppressor of Ras 2: A
Dual specificity mitogen-activated protein kinase kinase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Kinase suppressor of Ras 2

Dual specificity mitogen-activated protein kinase kinase 1

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