9GDI: Human PI3KDELTA

Human PI3KDELTA in complex with isocumarin inhibitor 10. Determined by X-ray diffraction at 2.81 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 8,947
Mol. weight: 141.17 kDa
Ligands: A1IJ1
Released: 18 Dec 2024

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

Secondary structure: helices and β-sheets

9GDI contains 55 α-helices and 44 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: 52 helices, 44 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	79-81	3	1
β-strand	88	1	2
α-helix	89-92	4
β-strand	98-103	6	1
α-helix	108-121	14
α-helix	126-130	5
α-helix	134-156	23
α-helix	159-166	8
β-strand	171	1	3
β-strand	189-196	8	4
β-strand	203-208	6	4
α-helix	213-224	12
α-helix	236-238	3
β-strand	239-242	4	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
β-strand	273-278	6	4
α-helix	279-286	8
α-helix	321	1
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
α-helix	365	1
β-strand	370-380	11	6
β-strand	389-397	9	7
α-helix	398-400	3
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
α-helix	441	1
β-strand	442-443	2	7
α-helix	444	1
α-helix	461-462	2
β-strand	470-475	6	6
α-helix	482-483	2
β-strand	484	1	9
α-helix	485-487	3
α-helix	488-497	10
α-helix	506-515	10
α-helix	525-533	9
α-helix	535-541	7
α-helix	543-545	3
α-helix	546-552	7
α-helix	558-569	12
α-helix	571-575	5
α-helix	576-582	7
α-helix	590-600	11
α-helix	605-618	14
α-helix	619-621	3
α-helix	628-639	12
α-helix	641-652	12
α-helix	658-673	16
α-helix	676-705	30
α-helix	708-719	12
α-helix	722-728	7
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	11
β-strand	759-764	6	11
β-strand	774-780	7	11
α-helix	785-803	19
β-strand	815-819	5	11
β-strand	822-826	5	11
β-strand	831-833	3	12
α-helix	834-838	5
α-helix	854-862	9
α-helix	865-867	3
α-helix	868-888	21
β-strand	899-902	4	12
β-strand	907-909	3	12
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
β-strand	986	1	13
β-strand	989	1	13
α-helix	992-1001	10
α-helix	1008-1025	18

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	442-512	71
α-helix	519-587	69
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	170	Bos taurus	P23727 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9GDI_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

>9GDI_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B)
YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNET
IKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLK
KQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN

Ligands and cofactors

ID	Name	Formula	Copies
A1IJ1	3-[(1S)-1-[4-azanyl-3-(3-fluoranyl-5-oxidanyl-phenyl)pyrazolo[3,4-d]pyrimidin-1…	C28 H25 F N6 O3	1

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

Primary citation

Discovery of CHF-6523, an Inhaled Selective PI3K delta Inhibitor for the Treatment of Chronic Obstructive Pulmonary Disease. Bruno, P., Pala, D., Micoli, A. et al. J Med Chem (2025) 68:2444-2465. DOI 10.1021/acs.jmedchem.4c02062 · 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
9L3R 2.5 Å, Human PI3KDELTA in complex with Zandelisib
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

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