5DXH: P110alpha/p85alpha with compound 5

p110alpha/p85alpha with compound 5. Determined by X-ray diffraction at 3.0 Å resolution. Released 27 Jan 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Bos taurus
Chains: 4
Atoms: 18,333
Mol. weight: 291.29 kDa
Ligands: 5H2
Released: 27 Jan 2016

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

Secondary structure: helices and β-sheets

5DXH contains 112 α-helices and 89 β-strands across 4 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, 46 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
β-strand	13	1	1
β-strand	19-25	7	2
β-strand	31-37	7	2
β-strand	41	1	3
α-helix	42-53	12
α-helix	59-61	3
α-helix	65-67	3
β-strand	69-73	5	2
β-strand	74	1	4
β-strand	79-82	4	2
β-strand	88	1	3
α-helix	89-91	3
β-strand	94	1	4
β-strand	98-102	5	2
α-helix	108-121	14
α-helix	126-130	5
α-helix	134-142	9
α-helix	144-154	11
α-helix	158-166	9
β-strand	171	1	5
α-helix	176-178	3
α-helix	179-182	4
α-helix	186-188	3
β-strand	189-198	10	6
β-strand	203-212	10	6
α-helix	217-229	13
α-helix	236-246	11
β-strand	250-254	5	6
β-strand	260	1	6
α-helix	267-269	3
β-strand	270	1	5
α-helix	271-279	9
α-helix	281-283	3
β-strand	284-289	6	6
α-helix	290-294	5
β-strand	324-326	3	7
β-strand	333-342	10	8
β-strand	353-362	10	9
β-strand	365-366	2	9
β-strand	371-372	2	9
β-strand	376-377	2	9
β-strand	382-392	11	8
α-helix	393-395	3
β-strand	400-409	10	9
β-strand	419-428	10	9
β-strand	430	1	10
β-strand	435	1	7
β-strand	436	1	10
α-helix	437	1
β-strand	439-444	6	8
α-helix	445	1
β-strand	446-447	2	9
α-helix	448-449	2
β-strand	462	1	9
β-strand	472-477	6	8
β-strand	483-485	3	7
α-helix	486-488	3
α-helix	489-496	8
α-helix	525-536	12
α-helix	545-553	9
α-helix	557-560	4
α-helix	562-564	3
α-helix	565-569	5
α-helix	577-588	12
α-helix	590-592	3
α-helix	595-598	4
α-helix	600-602	3
α-helix	609-622	14
α-helix	625-630	6
α-helix	632-637	6
α-helix	638-641	4
α-helix	648-657	10
α-helix	661-672	12
α-helix	681-694	14
α-helix	698-720	23
α-helix	728-740	13
α-helix	742-747	6
β-strand	751-752	2	11
β-strand	760-761	2	11
β-strand	764	1	12
α-helix	766-768	3
β-strand	770-771	2	12
β-strand	779-784	6	12
α-helix	790-792	3
β-strand	796-803	8	12
α-helix	808-827	20
β-strand	838-842	5	12
β-strand	845-849	5	12
β-strand	854-856	3	13
α-helix	857-861	5
α-helix	876-884	9
α-helix	889-911	23
β-strand	921-924	4	13
β-strand	929-931	3	13
α-helix	958-964	7
α-helix	975-992	18
α-helix	995-1003	9
α-helix	1016-1025	10
α-helix	1032-1045	14

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	458-513	56
α-helix	518-576	59

Chain D: 54 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	14
β-strand	13	1	14
β-strand	19-25	7	15
β-strand	31-37	7	15
β-strand	41	1	16
α-helix	42-53	12
α-helix	65-67	3
β-strand	69-73	5	15
β-strand	74	1	17
β-strand	79-82	4	15
β-strand	88	1	16
α-helix	89-91	3
β-strand	94	1	17
β-strand	98-102	5	15
α-helix	108-121	14
α-helix	126-130	5
α-helix	134-142	9
α-helix	144-155	12
α-helix	158-166	9
β-strand	171	1	18
α-helix	176-178	3
α-helix	179-182	4
α-helix	186-188	3
β-strand	189-198	10	19
β-strand	203-212	10	19
α-helix	217-229	13
α-helix	236-245	10
β-strand	250-254	5	19
β-strand	260	1	19
α-helix	267-269	3
β-strand	270	1	18
α-helix	271-279	9
α-helix	281-283	3
β-strand	284-289	6	19
α-helix	290-294	5
β-strand	324-326	3	20
β-strand	333-342	10	21
β-strand	355-362	8	22
β-strand	365-372	8	22
β-strand	382-392	11	21
α-helix	393-395	3
β-strand	400-408	9	22
β-strand	420-428	9	22
β-strand	430	1	23
β-strand	435	1	20
β-strand	436	1	23
α-helix	437	1
β-strand	439-444	6	21
α-helix	445	1
β-strand	446-447	2	22
α-helix	448-449	2
β-strand	472-477	6	21
β-strand	483-485	3	20
α-helix	486-488	3
α-helix	489-496	8
α-helix	525-536	12
α-helix	545-553	9
α-helix	557-560	4
α-helix	562-564	3
α-helix	565-569	5
α-helix	577-588	12
α-helix	590-592	3
α-helix	595-598	4
α-helix	600-602	3
α-helix	609-622	14
α-helix	625-630	6
α-helix	632-637	6
α-helix	638-641	4
α-helix	648-657	10
α-helix	661-673	13
α-helix	674-676	3
α-helix	681-694	14
α-helix	698-720	23
α-helix	728-740	13
α-helix	742-747	6
β-strand	751-753	3	24
β-strand	756-761	6	24
β-strand	764	1	25
α-helix	766-768	3
β-strand	770-771	2	25
β-strand	779-784	6	25
α-helix	790-792	3
β-strand	796-803	8	25
α-helix	808-826	19
β-strand	838-842	5	25
β-strand	845-849	5	25
β-strand	854-856	3	26
α-helix	857-861	5
α-helix	876-884	9
α-helix	889-911	23
β-strand	921-924	4	26
β-strand	929-931	3	26
α-helix	958-964	7
α-helix	975-993	19
α-helix	995-1003	9
α-helix	1016-1025	10
α-helix	1032-1045	14

Chain E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	454-514	61
α-helix	518-573	56

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A, D	protein	1067	Homo sapiens	P42336 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	B, E	protein	169	Bos taurus	P23727 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5DXH_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A, D)
PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQL
LQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAI
GMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHI
YNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKL
CVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDC
FTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIY
HGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCP
LAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFS
SVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLS
EITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMEL
LDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQ
RIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQ
EKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWL
NWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSI
GDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSC
AGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFL
IVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAY
IRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALN

Sequence of entity 2 (B, E), FASTA

>5DXH_2 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains B, E)
YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNET
IKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLK
KQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLG

Ligands and cofactors

ID	Name	Formula	Copies
5H2	methyl {2-[4-(2-chlorophenyl)-4H-1,2,4-triazol-3-yl]-4,5-dihydrothieno[3,2-d][1…	C22 H17 Cl N4 O3 S	2

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 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

Browse structure collections

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