9CMK: P110alpha-RAS binding domain

Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue D927. Determined by X-ray diffraction at 1.75 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,624
Mol. weight: 34.34 kDa
Ligands: MRD, MG, A1ATF
Released: 23 Jul 2025

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

Secondary structure: helices and β-sheets

9CMK contains 23 α-helices and 22 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	166	1	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
β-strand	294	1	4
α-helix	295-297	3

Chain B: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	162-163	2	5
β-strand	164	1	1
β-strand	166	1	4
α-helix	167-169	3
β-strand	171	1	6
α-helix	177-178	2
α-helix	179-182	4
β-strand	186	1	7
β-strand	189-197	9	7
β-strand	204-212	9	7
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	7
β-strand	260	1	7
α-helix	267-269	3
β-strand	270	1	6
α-helix	271-279	9
α-helix	281-283	3
β-strand	284-289	6	7
α-helix	290-293	4
β-strand	295-296	2	5

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

>9CMK_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A, B)
HSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQ
VIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIML
GRMPNLMLMAKESLYSQLPMD

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	2
MG	Magnesium ion	Mg	3
A1ATF	2-[3-fluoro-4-({(7P)-7-[2-(2-methoxyethoxy)phenyl]thieno[2,3-d]pyridazin-4-yl}a…	C23 H21 F N4 O3 S	2

Water and common crystallization additives (MPD) are not listed.

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:

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
9CML 2.01 Å, Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue…
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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