6PYS: Human PI3Kalpha

Human PI3Kalpha 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 2.19 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,558
Mol. weight: 110.61 kDa
Ligands: P5J
Released: 28 Aug 2019

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

Secondary structure: helices and β-sheets

6PYS contains 53 α-helices and 34 β-strands across 1 chain. 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: 53 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	108-121	14
α-helix	126-129	4
α-helix	134-154	21
α-helix	160-166	7
β-strand	171	1	1
α-helix	179-182	4
β-strand	189-197	9	2
β-strand	204-212	9	2
α-helix	217-230	14
β-strand	250-254	5	2
β-strand	260	1	2
α-helix	267-269	3
β-strand	270	1	1
α-helix	271-279	9
β-strand	284-289	6	2
α-helix	290-296	7
α-helix	303-305	3
α-helix	306-308	3
β-strand	323-326	4	3
α-helix	327-329	3
β-strand	333-342	10	4
β-strand	354-362	9	5
β-strand	365-366	2	5
β-strand	371-372	2	5
α-helix	373-375	3
β-strand	376	1	5
β-strand	382-392	11	4
α-helix	393-395	3
β-strand	401-408	8	5
β-strand	420-428	9	5
β-strand	430	1	6
β-strand	435	1	3
β-strand	436	1	6
α-helix	437	1
β-strand	439-444	6	4
β-strand	446-447	2	5
α-helix	448-449	2
α-helix	461-462	2
β-strand	472-477	6	4
β-strand	482-485	4	3
α-helix	486-488	3
α-helix	489-504	16
α-helix	508-511	4
α-helix	520-522	3
α-helix	525-535	11
α-helix	542-544	3
α-helix	545-553	9
α-helix	557-560	4
α-helix	562-564	3
α-helix	565-571	7
α-helix	577-588	12
α-helix	590-592	3
α-helix	595-600	6
α-helix	609-622	14
α-helix	625-630	6
α-helix	632-637	6
α-helix	638-641	4
α-helix	648-659	12
α-helix	661-672	12
α-helix	681-694	14
α-helix	698-721	24
α-helix	728-739	12
α-helix	742-747	6
β-strand	751-752	2	7
β-strand	760-761	2	7
β-strand	764	1	8
β-strand	770-771	2	8
β-strand	779-784	6	8
α-helix	790-792	3
β-strand	796-803	8	8
α-helix	808-826	19
β-strand	838-842	5	8
β-strand	845-849	5	8
α-helix	850-851	2
β-strand	854-856	3	9
α-helix	857-861	5
α-helix	876-884	9
α-helix	887-889	3
α-helix	890-911	22
α-helix	913-916	4
β-strand	921-924	4	9
β-strand	929-931	3	9
α-helix	958-964	7
α-helix	975-992	18
α-helix	995-1003	9
α-helix	1016-1025	10
α-helix	1032-1047	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	protein	945	Homo sapiens	P42336 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PYS_1 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (chains A)
NREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYV
YPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIR
KKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLM
LMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNV
NIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSI
CSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNP
NKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELREN
DKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCL
VKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLD
NLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQV
EAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRL
EECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQN
QGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNK
GEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFG
YKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMML
GSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGW

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

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

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 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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