SMTL ID : 9axm.1

Crystal structure of ARAF/MEK1 complex with NST-628 and a RAF dimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 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: 24 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, C.172, D.173, F.174, G.175, V.176, S.177, L.180, I.181, M.184, R.199 Chain B: G.217, C.218, R.219 Ligands: EDO.6 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.80, A:I.106, A:F.174, A:V.176, A:L.180, A:L.180, A:I.181 Hydrogen bonds: A:R.154, A:D.173, A:V.176, A:S.177, A:R.199, B:R.219 Water bridges: A:M.184 Halogen bonds: A:L.180, A:I.181 01.7: 22 residues within 4Å: Chain C: 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, M.195 Chain D: G.217, C.218, R.219 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.92, C:F.174, C:V.176, C:L.180, C:I.181 Hydrogen bonds: C:D.173, C:V.176, C:S.177, D:G.217, D:R.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.62, S.159, N.160, D.173 Ligands: ANP.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, H2O.1 MG.4: 3 residues within 4Å: Chain B: N.138, D.151 Ligands: ANP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.151, H2O.2

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

ANP.3: 22 residues within 4Å: Chain A: L.39, G.40, A.41, G.42, G.45, V.47, A.60, K.62, M.108, E.109, H.110, M.111, S.115, D.117, Q.118, D.155, K.157, S.159, N.160, L.162, D.173 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.62, A:E.109, A:M.111, A:S.115, A:S.115, A:S.115, A:D.155, A:K.157, A:S.159, A:N.160 Salt bridges: A:K.62 ANP.5: 20 residues within 4Å: Chain B: I.20, G.21, G.23, S.24, F.25, G.26, V.28, A.38, K.40, L.71, T.86, Q.87, W.88, C.89, D.133, K.135, N.138, F.140, D.151 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.23, B:S.24, B:F.25, B:K.40, B:K.40, B:T.86, B:Q.87, B:C.89, B:K.135, B:N.138 Salt bridges: B:K.40

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

EDO.6: 6 residues within 4Å: Chain A: G.190, R.192, I.237 Chain B: R.219, D.220 Ligands: 01.1 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.219, A:G.190 Water bridges: B:D.220, A:N.43

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain C: D.155, K.157, S.159, N.160, D.173 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.155, C:K.157, C:S.159, C:N.160, C:D.173 GOL.9: 5 residues within 4Å: Chain D: A.38, Q.87, W.88, C.89, F.140 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.87, D:C.89, D:C.89 GOL.10: 6 residues within 4Å: Chain B: W.7, R.63, R.66 Chain D: W.7, R.63, R.66 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.63, B:R.63, B:R.66, D:R.63, D:R.63, D:R.66, D:R.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryan, M.B. et al., The pan-RAF-MEK non degrading 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: AC
Serine/threonine-protein kinase A-Raf: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Dual specificity mitogen-activated protein kinase kinase 1

Serine/threonine-protein kinase A-Raf

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