SMTL ID : 9axx.1

Crystal structure of BRAF/MEK1 complex with NST-628 and an active RAF dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-2-2-mer

Ligands

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

ANP.1: 12 residues within 4Å: Chain A: I.20, T.27, V.28, A.38, K.40, L.71, T.86, Q.87, W.88, C.89, F.140 Chain B: H.65 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.27, A:V.28, A:T.86, A:Q.87, A:C.89 Water bridges: A:S.93 Salt bridges: A:K.40 ANP.8: 20 residues within 4Å: Chain B: L.39, 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.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.43, B:E.109, B:M.111, B:S.115, B:S.115, B:S.115, B:Q.118, B:K.157, B:S.159 Salt bridges: B:K.62 ANP.12: 19 residues within 4Å: Chain C: L.39, G.40, A.41, G.42, N.43, V.47, A.60, K.62, M.108, E.109, M.111, S.115, Q.118, K.157, S.159, N.160, L.162, D.173 Ligands: MG.13 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.42, C:N.43, C:N.43, C:E.109, C:M.111, C:S.115, C:S.115, C:S.115, C:K.157, C:S.159, C:S.159 Water bridges: C:A.41, C:G.44, C:Q.118, C:F.188 Salt bridges: C:K.62

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: D.6, W.7, R.63 Chain D: W.7, R.63 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.63, D:R.63, A:R.63, A:R.63

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

EDO.3: 4 residues within 4Å: Chain A: I.216, Q.221, M.225, L.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.221 EDO.4: 6 residues within 4Å: Chain A: K.40, E.58, L.62, L.71, D.151, F.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.58, A:F.152 Water bridges: A:K.40 EDO.5: 7 residues within 4Å: Chain A: I.14, V.16, M.41, S.77, P.80, Q.81, A.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:S.77, A:Q.81 EDO.6: 5 residues within 4Å: Chain A: A.126, K.127 Chain D: Q.13, W.33, H.34 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.13, D:H.34, A:K.127 EDO.10: 8 residues within 4Å: Chain B: I.228, Y.243, I.244, E.247, P.248, P.249, P.250, K.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.244 EDO.14: 7 residues within 4Å: Chain C: V.189, I.237 Chain D: S.171, I.174, M.177, V.181, I.182 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:I.237 Hydrogen bonds: D:S.171, D:I.182 EDO.15: 4 residues within 4Å: Chain D: K.40, L.71, F.140, D.151 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.40, D:D.151 Water bridges: D:E.58, D:T.86 EDO.16: 6 residues within 4Å: Chain D: V.28, A.38, Q.87, W.88, C.89, F.140 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.87, D:C.89 EDO.17: 8 residues within 4Å: Chain D: I.14, V.16, M.41, S.77, K.79, P.80, Q.81, A.83 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.77, D:Q.81, D:Q.81 EDO.18: 8 residues within 4Å: Chain D: F.25, K.40, L.42, Q.51, F.55, L.82, A.83, I.84 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.42, D:Q.51, D:I.84 EDO.19: 3 residues within 4Å: Chain C: Q.201 Chain D: F.224, Y.230 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:Q.201 Hydrogen bonds: D:Y.230

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

01.7: 22 residues within 4Å: Chain A: N.217, N.218 Chain B: L.80, L.83, V.92, 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: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.80, B:V.92, B:I.106, 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 Water bridges: B:M.184, A:R.219, A:R.219, A:R.219 Halogen bonds: B:I.181 01.11: 23 residues within 4Å: Chain C: 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 Chain D: N.217, N.218 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.80, C:F.174, C:L.180, C:I.181 Hydrogen bonds: C:R.154, C:D.173, C:V.176, C:S.177, C:R.199, D:R.219 Water bridges: C:R.154 Halogen bonds: C:I.181

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain B: S.159, N.160, D.173 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.173 MG.13: 4 residues within 4Å: Chain C: K.62, N.160, D.173 Ligands: ANP.12 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.173

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

Serine/threonine-protein kinase B-raf: AD
Dual specificity mitogen-activated protein kinase kinase 1: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
D

B
C

C
A

Serine/threonine-protein kinase B-raf

Dual specificity mitogen-activated protein kinase kinase 1

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