9CML: P110alpha-RAS binding domain

Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue D223. Determined by X-ray diffraction at 2.01 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,430
Mol. weight: 34.17 kDa
Ligands: A1AZD
Released: 23 Jul 2025

Explore 9CML in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CML contains 24 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	165-166	2	1
α-helix	167-169	3
β-strand	171	1	2
α-helix	177-178	2
α-helix	179-182	4
β-strand	186	1	3
β-strand	189-197	9	3
β-strand	204-212	9	3
α-helix	217-228	12
α-helix	230-232	3
α-helix	236-246	11
α-helix	247-249	3
β-strand	250-254	5	3
β-strand	260	1	3
α-helix	267-269	3
β-strand	270	1	2
α-helix	271-279	9
α-helix	281-283	3
β-strand	284-289	6	3
α-helix	290-293	4
α-helix	294-297	4

Chain B: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	162-163	2	4
β-strand	164-165	2	1
α-helix	167-169	3
β-strand	171	1	5
α-helix	176-178	3
α-helix	179-182	4
β-strand	186	1	6
β-strand	189-197	9	6
β-strand	204-212	9	6
α-helix	217-228	12
α-helix	230-232	3
α-helix	236-246	11
β-strand	250-254	5	6
β-strand	260	1	6
α-helix	267-269	3
β-strand	270	1	5
α-helix	271-279	9
α-helix	281-283	3
β-strand	284-289	6	6
α-helix	290-293	4
α-helix	294	1
β-strand	295-296	2	4
α-helix	297-298	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A, B	protein	141	Homo sapiens	P42336 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9CML_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A, B)
HSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQ
VIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIML
GRMPNLMLMAKESLYSQLPMD

Ligands and cofactors

ID	Name	Formula	Copies
A1AZD	tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3…	C29 H32 F N5 O5 S	2

Primary citation

Molecular glues that facilitate RAS binding to PI3K alpha promote glucose uptake without insulin. Terayama, K., Furuzono, S., Fer, N. et al. Science (2025) 389:402-408. DOI 10.1126/science.adr9097 · PubMed

Other PDB entries of the same protein (UniProt P42336 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CMK 1.75 Å, Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue…
9ASF 1.77 Å, Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide analogue…
9CX0 1.92 Å, Crystal structure of HLA-A*03:01 E152V mutant in complex with a mutant PIK3CA peptide
7L1C 1.96 Å, Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide
9CWY 1.98 Å, Crystal structure of HLA-A*03:02 in complex with a wild-type PIK3CA peptide
8EXL 1.99 Å, Crystal structure of PI3K-alpha in complex with taselisib
9CX1 2.0 Å, Crystal structure of HLA-A*03:01 L156Q mutant in complex with a mutant PIK3CA peptide
9ASG 2.03 Å, Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6…
7L1B 2.04 Å, Crystal structure of HLA-A*03:01 in complex with a wild-type PIK3CA peptide
9CWZ 2.05 Å, Crystal structure of HLA-A*03:02 in complex with a mutant PIK3CA peptide
7JIU 2.12 Å, Human PI3KDELTA in complex with compound 2F
7RRG 2.12 Å, Crystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in complex with a mutant…

Browse structure collections

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