6JOI

Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization

PDB DOI: https://doi.org/10.2210/pdb6JOI/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2019-03-22 Released: 2020-03-25
Deposition Author(s): Liang, L., Yan, X.E., Yun, C.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.244
R-Value Work: 0.223
R-Value Observed: 0.224

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization

Liang, L., Yan, X.E.

To be published.

Macromolecule Content

Total Structure Weight: 43.47 kDa
Atom Count: 2,410
Modelled Residue Count: 296
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor alpha	A	375	Homo sapiens	Mutation(s): 1 Gene Names: PDGFRA, PDGFR2, RHEPDGFRA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P16234 (Homo sapiens) Explore P16234 Go to UniProtKB: P16234
PHAROS: P16234 GTEx: ENSG00000134853
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16234
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6T2 Query on 6T2 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine C₂₆ H₂₉ N₅ O₂ DYNHJHQFHQTFTP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.244
R-Value Work: 0.223
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.757	α = 90
b = 73.992	β = 90
c = 103.706	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.