5XGJ | pdb_00005xgj

Crystal structure of PI3K complex with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb5XGJ/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-04-13 Released: 2018-04-25
Deposition Author(s): Song, K., Yang, X., Zhao, Y., Jian, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.279 (Depositor), 0.288 (DCC)
R-Value Work:
0.231 (Depositor)
R-Value Observed:
0.233 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of PI3K complex with an inhibitor

Song, K., Yang, X., Zhao, Y., Jian, Z.

To be published.

Macromolecule Content

Total Structure Weight: 156.13 kDa
Atom Count: 10,430
Modeled Residue Count: 1,258
Deposited Residue Count: 1,326
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	1,048	Homo sapiens	Mutation(s): 0 Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336 Go to UniProtKB: P42336
PHAROS: P42336 GTEx: ENSG00000121879
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42336
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	278	Homo sapiens	Mutation(s): 0 Gene Names: PIK3R1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986 Go to UniProtKB: P27986
PHAROS: P27986 GTEx: ENSG00000145675
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
84X Query on 84X Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3-(4-morpholin-4-ylfuro[3,2-d]pyrimidin-2-yl)-5-[(phenylmethyl)amino]phenol C₂₃ H₂₂ N₄ O₃ NOLJEVWXVAGNIQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free: 0.279 (Depositor), 0.288 (DCC)
R-Value Work: 0.231 (Depositor)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.877	α = 90
b = 136.368	β = 90
c = 149.028	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-04-25
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.