SMTL ID : 9ay7.1

Crystal structure of CRAF/MEK1 complex with NST-628 and inactive RAF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

hetero-1-1-mer

Ligands

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

ANP.1: 21 residues within 4Å: Chain A: I.20, G.21, S.22, G.23, S.24, F.25, G.26, V.28, A.38, K.40, L.71, T.86, Q.87, W.88, C.89, K.135, N.137, N.138, F.140, D.151 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.24, A:F.25, A:K.40, A:K.40, A:K.40, A:T.86, A:Q.87, A:C.89, A:K.135, A:N.137, A:N.138 Water bridges: A:G.23, A:S.93, A:S.93 Salt bridges: A:K.40 pi-Stacking: A:W.88 ANP.8: 21 residues within 4Å: Chain B: L.75, G.76, A.77, G.78, N.79, G.80, G.81, V.83, A.96, K.98, M.144, E.145, M.147, S.151, Q.154, K.193, S.195, N.196, L.198, D.209 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.79, B:G.80, B:E.145, B:M.147, B:S.151, B:S.151, B:S.151, B:K.193, B:S.195, B:S.195 Water bridges: B:A.77, B:Q.154 Salt bridges: B:K.98

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.138, D.151 Ligands: ANP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, H2O.2 MG.9: 4 residues within 4Å: Chain B: K.98, N.196, D.209 Ligands: ANP.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.209, H2O.4, H2O.5

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: E.272, Q.275, H.276 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.272, A:H.276, H2O.3

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: P.265, Q.266, S.269 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.265 Hydrogen bonds: A:S.269 ACT.5: 8 residues within 4Å: Chain A: R.219, D.220 Chain B: D.191, K.193, S.229, Y.230, M.231 Ligands: 01.7 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.193 Hydrogen bonds: B:Y.230, B:M.231 Water bridges: B:D.191 Salt bridges: B:K.193, A:R.219 ACT.10: 4 residues within 4Å: Chain B: E.39, E.40, L.41, E.42 No protein-ligand interaction detected (PLIP) ACT.11: 4 residues within 4Å: Chain B: K.169, G.203, V.370, F.372 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.169 Hydrogen bonds: B:G.203 Water bridges: B:F.372 ACT.12: 5 residues within 4Å: Chain A: R.219 Chain B: N.79, M.220, A.223 Ligands: 01.7 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.219 Salt bridges: A:R.219 Hydrogen bonds: B:N.79 Water bridges: B:G.80

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

EDO.6: 3 residues within 4Å: Chain A: F.105, Y.239, N.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:N.241

1 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

01.7: 26 residues within 4Å: Chain A: N.217, N.218, R.219 Chain B: L.116, L.119, V.128, G.129, F.130, I.142, M.144, H.189, R.190, D.191, C.208, D.209, F.210, G.211, V.212, S.213, L.216, I.217, M.220, M.231, R.235 Ligands: ACT.5, ACT.12 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:R.219, B:R.190, B:D.209, B:V.212, B:S.213, B:R.235, B:R.235 Hydrophobic interactions: B:L.116, B:L.119, B:I.142, B:F.210, B:L.216, B:L.216, B:I.217 Water bridges: B:R.190 Halogen bonds: B:I.217

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

RAF proto-oncogene serine/threonine-protein kinase: A
Dual specificity mitogen-activated protein kinase kinase 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RAF proto-oncogene serine/threonine-protein kinase

Dual specificity mitogen-activated protein kinase kinase 1

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