SMTL ID : 9axh.1

Crystal structure of KSR1/MEK1 complex heterotetramer with NST-628

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 01: N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide

01.1: 23 residues within 4Å: Chain A: L.80, L.83, V.92, G.93, F.94, I.106, M.108, H.153, R.154, D.155, L.171, C.172, D.173, F.174, G.175, V.176, S.177, L.180, I.181, M.184, A.185, R.199 Chain D: A.226 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.80, A:I.106, A:D.173, A:L.180, A:I.181 Hydrogen bonds: A:R.154, A:D.173, A:F.174, A:V.176, A:S.177, A:R.199, A:R.199 pi-Stacking: A:F.174 Halogen bonds: A:I.181 01.4: 24 residues within 4Å: Chain B: K.62, L.80, L.83, V.92, G.93, F.94, I.106, M.108, H.153, R.154, D.155, C.172, D.173, F.174, G.175, V.176, S.177, L.180, I.181, M.184, A.185, R.199 Chain C: A.226 Ligands: CL.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.80, B:V.92, B:I.106, B:D.173, B:F.174, B:L.180, B:L.180, B:I.181 Hydrogen bonds: B:R.154, B:D.173, B:V.176, B:S.177, B:R.199, B:R.199 Halogen bonds: B:I.181

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

ANP.2: 21 residues within 4Å: Chain A: L.39, G.40, A.41, G.42, N.43, G.45, V.47, A.60, K.62, M.108, E.109, H.110, M.111, S.115, Q.118, K.157, S.159, N.160, L.162, D.173 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.42, A:E.109, A:H.110, A:M.111, A:S.115, A:S.115, A:K.157, A:K.157, A:S.159, A:S.159 Water bridges: A:N.160 Salt bridges: A:K.62 ANP.5: 22 residues within 4Å: Chain B: L.39, G.40, A.41, G.42, N.43, G.45, V.47, A.60, K.62, M.108, E.109, H.110, M.111, S.115, Q.118, D.155, K.157, S.159, N.160, L.162, D.173 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.42, B:E.109, B:M.111, B:S.115, B:S.115, B:S.115, B:K.157, B:S.159 Water bridges: B:K.62, B:N.160 Salt bridges: B:K.62 ANP.7: 18 residues within 4Å: Chain C: A.38, R.40, T.87, S.88, F.89, C.90, T.94, K.136, K.138, N.139, F.141, D.151 Chain D: G.21, Q.22, G.23, R.24, V.28 Ligands: MG.8 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.87, C:S.88, C:C.90, C:K.136, D:R.24 Water bridges: C:N.139, C:N.139, C:T.150 Salt bridges: C:R.40 ANP.11: 16 residues within 4Å: Chain C: I.20, G.23, R.24 Chain D: A.38, R.40, T.87, S.88, F.89, C.90, T.94, K.136, K.138, N.139, F.141, D.151 Ligands: MG.12 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.87, D:S.88, D:C.90, D:K.136, D:N.139, C:R.24 Water bridges: D:N.139, D:T.150 Salt bridges: D:R.40

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.159, N.160, D.173 Ligands: ANP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.173, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: S.159, N.160, D.173 Ligands: ANP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.173, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain C: R.40, N.139, D.151 Ligands: ANP.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.151, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain D: R.40, N.139, D.151 Ligands: ANP.11 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.151, H2O.1, H2O.1

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

EDO.9: 5 residues within 4Å: Chain C: K.120, G.123, Y.124, S.272, M.275 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain B: D.155, K.157 Chain C: E.228 Ligands: 01.4 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain D: S.272 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryan, M.B. et al., The Pan-RAF-MEK Nondegrading Molecular Glue NST-628 Is a Potent and Brain-Penetrant Inhibitor of the RAS-MAPK Pathway with Activity across Diverse RAS- and RAF-Driven Cancers. Cancer Discov (2024)

Release Date

2024-04-17

Peptides

Dual specificity mitogen-activated protein kinase kinase 1: AB
Kinase suppressor of Ras 1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dual specificity mitogen-activated protein kinase kinase 1

Kinase suppressor of Ras 1