9B4U: P110alpha-RBD covalently

Crystal structure of p110alpha-RBD covalently bound to a breaker compound BBO-10203 via Cys242. Determined by X-ray diffraction at 2.21 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,419
Mol. weight: 34.89 kDa
Ligands: A1AIR
Released: 25 Jun 2025

Explore 9B4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B4U contains 17 α-helices and 16 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	159-166	8
β-strand	171	1	1
α-helix	177-178	2
α-helix	179-182	4
β-strand	186	1	2
β-strand	189-197	9	2
β-strand	204-212	9	2
α-helix	217-228	12
α-helix	229-231	3
α-helix	236-247	12
β-strand	250-254	5	2
β-strand	260	1	2
α-helix	267-269	3
β-strand	270	1	1
α-helix	271-279	9
β-strand	284-289	6	2
α-helix	290-295	6

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	159-166	8
β-strand	171	1	3
α-helix	177-178	2
α-helix	179-182	4
β-strand	186	1	4
β-strand	189-197	9	4
β-strand	204-212	9	4
α-helix	217-228	12
α-helix	236-247	12
β-strand	250-254	5	4
β-strand	260-261	2	4
α-helix	267-269	3
β-strand	270	1	3
α-helix	271-278	8
β-strand	284-289	6	4
α-helix	290-295	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A, B	protein	144	Homo sapiens	P42336 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9B4U_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A, B)
NSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCV
PEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSC
IMLGRMPNLMLMAKESLYSQLPMD

Ligands and cofactors

ID	Name	Formula	Copies
A1AIR	1-[(4R,8R)-2-[(4M,7P)-7-[2,4-difluoro-6-(2-methoxyethoxy)phenyl]-4-(1-methyl-1H…	C34 H32 F2 N6 O3 S	2

Primary citation

BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3K alpha interaction. Simanshu, D.K., Xu, R., Stice, J.P. et al. Science (2025) 389:409-415. DOI 10.1126/science.adq2004 · 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
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

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