SMTL ID : 9c15.1

Crystal structure of the KRAS-p110alpha complex with molecular glue D927

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: 2-[3-fluoro-4-({(7P)-7-[2-(2-methoxyethoxy)phenyl]thieno[2,3-d]pyridazin-4-yl}amino)phenyl]acetamide

01.1: 14 residues within 4Å: Chain A: I.91, V.93, Q.102, K.103, Y.104, A.121, I.122, K.125, Y.147, L.184 Chain B: I.25, Q.26, Y.41, R.42 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.93, A:Y.104, A:A.121, A:I.122, A:K.125, A:L.184, B:Y.41, B:Y.41 Hydrogen bonds: A:Q.102, A:Y.147, B:R.42, B:R.42 pi-Stacking: A:Y.104, A:Y.147

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: H.656 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

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 5 residues within 4Å: Chain A: P.506, R.509, E.539, L.545, L.546 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.509 IPA.4: 5 residues within 4Å: Chain A: N.693, N.694, E.695, V.747, R.749 No protein-ligand interaction detected (PLIP)

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

GNP.5: 24 residues within 4Å: Chain B: A.12, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, D.34, P.35, T.36, A.60, G.61, 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:K.17, B:S.18, B:A.19, B:V.30, B:D.31, B:Y.33, B:Y.33, B:D.34, B:T.36, B:G.61, B:N.117, B:A.147, B:K.148 Salt bridges: B:D.120 pi-Stacking: B:F.29, B:F.29 pi-Cation interactions: B:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czyzyk, D. et al., Structural insights into isoform-specific RAS-PI3K alpha interactions and the role of RAS in PI3K alpha activation. Nat Commun (2025)

Release Date

2025-01-22

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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