SMTL ID : 9cmv.1

Crystal structure of the KRAS-p110alpha complex in the presence of molecular glue D223

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate

01.1: 15 residues within 4Å: Chain A: I.91, V.93, Q.102, K.103, Y.104, A.121, I.122, K.125, Y.143, Y.147, L.184 Chain B: I.25, Q.26, Y.41, R.42 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.93, A:Y.104, A:I.122, A:Y.143, A:Y.143, A:L.184, B:I.25, B:Y.41, B:Y.41 Hydrogen bonds: A:Q.102, A:K.125, B:R.42, B:R.42 pi-Stacking: A:Y.104, A:Y.147 pi-Cation interactions: A:K.125

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: I.697, I.745, V.748, M.819, I.829 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.694, V.747, R.749 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: S.18, T.36, D.58 Ligands: GNP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.18, B:T.36

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.5: 26 residues within 4Å: Chain B: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, P.35, T.36, T.59, A.60, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.6 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.14, B:V.15, B:G.16, B:K.17, B:K.17, B:S.18, B:A.19, B:V.30, B:Y.33, B:T.36, B:T.36, B:T.59, B:G.61, B:Q.62, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terayama, K. et al., Molecular glues that facilitate RAS binding to PI3K alpha promote glucose uptake without insulin. Science (2025)

Release Date

2025-07-23

Peptides

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform: A
GTPase KRas: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

GTPase KRas

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