6PYR: Human PI3Kdelta

Human PI3Kdelta in complex with Compound 2-10 ((3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-dihydro-2H-indol-2-one). Determined by X-ray diffraction at 2.21 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,064
Mol. weight: 137.93 kDa
Ligands: P5J
Released: 28 Aug 2019

Explore 6PYR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PYR contains 57 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: 54 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	74	1	3
β-strand	79-81	3	1
β-strand	88	1	2
α-helix	89-92	4
β-strand	94	1	3
β-strand	98-103	6	1
α-helix	108-120	13
α-helix	126-129	4
α-helix	134-155	22
α-helix	159-166	8
β-strand	171	1	4
β-strand	189-196	8	5
β-strand	202-208	7	5
α-helix	213-225	13
β-strand	239-243	5	5
β-strand	246	1	6
β-strand	249-250	2	5
α-helix	256-258	3
β-strand	259	1	4
α-helix	260-268	9
α-helix	270-272	3
β-strand	273-278	6	5
α-helix	279-286	8
β-strand	322-331	10	7
β-strand	340-349	10	8
β-strand	352-353	2	8
α-helix	356-357	2
β-strand	358-359	2	8
α-helix	360-362	3
β-strand	363-364	2	8
β-strand	370-380	11	7
α-helix	381-383	3
β-strand	389-397	9	8
α-helix	398-400	3
β-strand	416-424	9	8
β-strand	426	1	9
β-strand	431	1	10
β-strand	432	1	9
α-helix	433	1
β-strand	435-440	6	7
β-strand	442-443	2	8
α-helix	444-445	2
α-helix	461-462	2
β-strand	470-475	6	7
α-helix	476-477	2
β-strand	484	1	10
α-helix	485-487	3
α-helix	488-495	8
α-helix	505-515	11
α-helix	522-524	3
α-helix	525-533	9
α-helix	535-541	7
α-helix	543-545	3
α-helix	546-552	7
α-helix	558-570	13
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	722-728	7
β-strand	731-732	2	11
β-strand	739	1	6
β-strand	740-741	2	11
β-strand	743-744	2	12
α-helix	746-748	3
β-strand	750-751	2	12
β-strand	759-764	6	12
β-strand	774-780	7	12
α-helix	785-803	19
β-strand	815-819	5	12
β-strand	822-826	5	12
β-strand	831-833	3	13
α-helix	834-839	6
α-helix	854-862	9
α-helix	865-867	3
α-helix	868-889	22
β-strand	899-902	4	13
β-strand	907-909	3	13
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	442-514	73
α-helix	518-586	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	1018	Homo sapiens	O00329 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	protein	169	Homo sapiens	P27986 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PYR_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (chains A)
NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQT
AEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEV
NDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKF
EGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPL
CQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSL
WSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLE
FDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGE
RCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGR
HSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWN
KHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLV
QVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGST
HHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLD
PSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQL
MDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALL
NWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFL
GNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLH
LFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVNWL

Sequence of entity 2 (B), FASTA

>6PYR_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B)
YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNET
IKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLK
KQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLG

Ligands and cofactors

ID	Name	Formula	Copies
P5J	(3S)-3-benzyl-3-methyl-5-[5-(2-methylpyrimidin-5-yl)pyrazolo[1,5-a]pyrimidin-3-…	C27 H22 N6 O	1

Primary citation

Design of selective PI3K delta inhibitors using an iterative scaffold-hopping workflow. Fradera, X., Methot, J.L., Achab, A. et al. Bioorg Med Chem Lett (2019) 29:2575-2580. DOI 10.1016/j.bmcl.2019.08.004 · PubMed

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

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
5VLR 2.8 Å, Crystal structure of PI3K delta in complex with a trifluoro-ethyl-pyrazol-pyrolotriazine…

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