9L3R: Human PI3KDELTA

Human PI3KDELTA in complex with Zandelisib. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 8,947
Mol. weight: 141.36 kDa
Ligands: A1L62
Released: 11 Jun 2025

Explore 9L3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L3R contains 52 α-helices and 45 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: 49 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	19-25	7	1
β-strand	31-37	7	1
β-strand	41	1	2
α-helix	42-53	12
α-helix	59-61	3
α-helix	65-67	3
β-strand	68-73	6	1
β-strand	79-82	4	1
β-strand	88	1	2
α-helix	89-92	4
β-strand	98-103	6	1
α-helix	109-120	12
α-helix	126-131	6
α-helix	134-154	21
α-helix	159-166	8
β-strand	171	1	3
β-strand	189-196	8	4
β-strand	202-208	7	4
α-helix	213-224	12
α-helix	236-238	3
β-strand	239-243	5	4
β-strand	246	1	5
β-strand	249-250	2	4
α-helix	256-258	3
β-strand	259	1	3
α-helix	260-268	9
α-helix	270-272	3
β-strand	273-278	6	4
α-helix	279-286	8
α-helix	316-318	3
β-strand	322-331	10	6
β-strand	340-349	10	7
β-strand	352-353	2	7
β-strand	358-359	2	7
β-strand	363-364	2	7
β-strand	370-380	11	6
α-helix	381-383	3
β-strand	389-397	9	7
β-strand	416-424	9	7
β-strand	426	1	8
β-strand	431	1	9
β-strand	432	1	8
α-helix	433	1
β-strand	435-440	6	6
β-strand	442-443	2	7
α-helix	461-462	2
β-strand	470-475	6	6
α-helix	476-477	2
β-strand	484	1	9
α-helix	485-487	3
α-helix	488-495	8
α-helix	506-514	9
α-helix	525-533	9
α-helix	535-541	7
α-helix	543-545	3
α-helix	546-552	7
α-helix	558-568	11
α-helix	571-575	5
α-helix	576-582	7
α-helix	590-600	11
α-helix	605-617	13
α-helix	618-621	4
α-helix	628-639	12
α-helix	641-652	12
α-helix	661-673	13
α-helix	676-703	28
α-helix	708-719	12
α-helix	722-727	6
β-strand	731-732	2	10
β-strand	739	1	5
β-strand	740-741	2	10
β-strand	743-744	2	11
β-strand	750-751	2	12
β-strand	759-762	4	12
β-strand	763-764	2	11
β-strand	775-780	6	12
α-helix	785-802	18
β-strand	815-819	5	12
β-strand	822-826	5	12
β-strand	831-833	3	13
α-helix	834-838	5
α-helix	854-862	9
α-helix	867-889	23
β-strand	899-902	4	13
β-strand	907-909	3	13
β-strand	918	1	14
β-strand	927	1	14
α-helix	929-932	4
α-helix	936-942	7
α-helix	950-969	20
α-helix	971-981	11
α-helix	982-984	3
α-helix	992-1001	10
α-helix	1008-1031	24

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	442-513	72
α-helix	518-587	70
α-helix	591-597	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	protein	1044	Homo sapiens	O00329 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	protein	172	Bos taurus	P23727 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9L3R_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (chains A)
MPPGVDCPMEFWTKEENQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFH
MLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLL
IGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGP
GTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYT
LQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPR
AKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSS
SEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAW
ANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAP
HPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQE
HFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSL
RKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSV
ALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMR
QEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKN
GDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLN
KSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIM
IRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYC
ERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFN
EALRESWKTKVNWLAHNVSKDNRQ

Sequence of entity 2 (B), FASTA

>9L3R_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B)
XMYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFN
ETIKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEED
LKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN

Ligands and cofactors

ID	Name	Formula	Copies
A1L62	Zandelisib	C31 H38 F2 N8 O	1

Primary citation

A long-lasting PI3K delta inhibitor zandelisib forms a water-shielded hydrogen bond with p110 delta and demonstrates sustained inhibitory effects. Kunieda, K., Nagiri, C., Watanabe, M. et al. Am J Cancer Res (2025) 15:2097-2110. DOI 10.62347/JCGQ1004 · PubMed

Other PDB entries of the same protein (UniProt O00329 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PYR 2.21 Å, Human PI3Kdelta in complex with Compound 2-10 ((3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrim…
8S3R 2.28 Å, Human PI3KDELTA in complex with pyridazinone inhibitor 7
7JIS 2.42 Å, Human PI3KDELTA in complex with compound 2F
8BCY 2.43 Å, Human PI3KDELTA in complex with compound 13
6PYU 2.54 Å, Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxali…
6OCO 2.58 Å, Human PI3KDELTA in complex with compound 6
5DXU 2.64 Å, p110delta/p85alpha with GDC-0326
6G6W 2.72 Å, Human PI3KDELTA in complex with ligand LASW1976
9T07 2.75 Å, HUMAN PI3KDELTA IN COMPLEX WITH Roginolisib
6OCU 2.77 Å, Human PI3KDELTA in complex with compound 29
7LM2 2.79 Å, Human PI3KDELTA in complex with compound 3C
5VLR 2.8 Å, Crystal structure of PI3K delta in complex with a trifluoro-ethyl-pyrazol-pyrolotriazine…

Browse structure collections

About this viewer

MolViewer shows 9L3R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.