SMTL ID : 9aya.1

Crystal structure of CRAF/MEK complex with NST-628 and active RAF dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 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: 25 residues within 4Å: Chain A: N.217, N.218, R.219 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, M.195, R.199 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:R.219, B:R.154, B:D.173, B:V.176, B:S.177, B:R.199, B:R.199 Hydrophobic interactions: B:L.80, B:L.83, B:V.92, B:V.92, B:I.106, B:D.173, B:F.174, B:L.180, B:L.180, B:I.181 Halogen bonds: B:I.181 01.4: 22 residues within 4Å: Chain C: N.217, N.218 Chain D: 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 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.80, D:I.106, D:F.174, D:L.180, D:L.180, D:I.181 Hydrogen bonds: D:R.154, D:D.173, D:V.176, D:S.177, D:R.199, D:R.199 Water bridges: D:D.155 Halogen bonds: D:I.181

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

ANP.2: 23 residues within 4Å: Chain B: L.39, G.40, A.41, G.42, N.43, G.44, 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.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.42, B:N.43, B:G.44, B:E.109, B:M.111, B:S.115, B:S.115, B:S.115, B:K.157, B:S.159, B:S.159 Water bridges: B:Q.118 Salt bridges: B:K.62 ANP.5: 18 residues within 4Å: Chain D: L.39, G.40, A.41, 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.6 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:E.109, D:H.110, D:M.111, D:S.115, D:S.115, D:S.115, D:K.157, D:K.157, D:S.159, D:S.159 Water bridges: D:Q.118, D:N.160 Salt bridges: D:K.62

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: N.160, D.173 Ligands: ANP.2 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.173, H2O.1 MG.6: 4 residues within 4Å: Chain D: K.62, N.160, D.173 Ligands: ANP.5 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.173, H2O.2, H2O.2

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: AC
Dual specificity mitogen-activated protein kinase kinase 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

RAF proto-oncogene serine/threonine-protein kinase

Dual specificity mitogen-activated protein kinase kinase 1

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