5DXU: P110delta/p85alpha with GDC-0326

p110delta/p85alpha with GDC-0326. Determined by X-ray diffraction at 2.64 Å resolution. Released 27 Jan 2016.

Method: X-ray diffraction
Resolution: 2.64 Å
Organisms: Homo sapiens, Bos taurus
Chains: 2
Atoms: 8,955
Mol. weight: 140.76 kDa
Ligands: 5H5
Released: 27 Jan 2016

Explore 5DXU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DXU contains 55 α-helices and 49 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, 49 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	79-82	4	1
β-strand	88	1	2
α-helix	89-92	4
β-strand	94	1	3
β-strand	98-103	6	1
α-helix	108-121	14
α-helix	126-130	5
α-helix	134-156	23
α-helix	159-166	8
β-strand	171	1	4
β-strand	189	1	5
β-strand	192-196	5	6
β-strand	202-205	4	6
β-strand	208	1	5
α-helix	213-221	9
α-helix	236-238	3
β-strand	239-243	5	6
β-strand	246	1	7
β-strand	248-250	3	6
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	6
α-helix	279-286	8
β-strand	322-331	10	8
β-strand	340-349	10	9
β-strand	352-353	2	9
β-strand	359	1	9
β-strand	363-364	2	9
α-helix	365	1
β-strand	370-380	11	8
β-strand	389-397	9	9
β-strand	416-424	9	9
β-strand	426	1	10
β-strand	431	1	11
β-strand	432	1	10
α-helix	433	1
β-strand	435-440	6	8
α-helix	441	1
β-strand	442-443	2	9
α-helix	444	1
α-helix	461-462	2
β-strand	470-475	6	8
β-strand	484	1	11
α-helix	485-487	3
α-helix	488-491	4
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	605-610	6
α-helix	612-618	7
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	708-720	13
α-helix	722-728	7
β-strand	731-732	2	12
β-strand	739	1	7
β-strand	740-741	2	12
β-strand	743-744	2	13
β-strand	750-751	2	14
β-strand	759-762	4	14
β-strand	763-764	2	13
β-strand	775-780	6	14
α-helix	785-802	18
β-strand	815-819	5	14
β-strand	822-826	5	14
α-helix	827-828	2
β-strand	831-833	3	15
α-helix	834-839	6
α-helix	854-862	9
α-helix	865-867	3
α-helix	868-888	21
β-strand	899-902	4	15
β-strand	907-909	3	15
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	16
β-strand	989	1	16
α-helix	992-1001	10
α-helix	1008-1030	23

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	442-513	72
α-helix	518-586	69
α-helix	591-598	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	protein	1043	Homo sapiens	O00329 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	protein	169	Bos taurus	P23727 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5DXU_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (chains A)
PPGVDCPMEFWTKEENQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHM
LSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLI
GKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPG
TLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTL
QVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRA
KPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSS
EVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWA
NLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPH
PVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEH
FPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLR
KLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVA
LRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQ
EAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNG
DDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNK
SNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMI
RESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCE
RAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNE
ALRESWKTKVNWLAHNVSKDNRQ

Sequence of entity 2 (B), FASTA

>5DXU_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B)
YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNET
IKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLK
KQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLG

Ligands and cofactors

ID	Name	Formula	Copies
5H5	(2S)-2-({2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,…	C19 H22 N6 O3	1

Primary citation

The Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepin-9-yl)oxy)propanamide (GDC-0326). Heffron, T.P., Heald, R.A., Ndubaku, C. et al. J Med Chem (2016) 59:985-1002. DOI 10.1021/acs.jmedchem.5b01483 · 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
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 5DXU 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.