8XRR | pdb_00008xrr

A complex structure of PDGFRA with an inhibitor RH140

PDB DOI: https://doi.org/10.2210/pdb8XRR/pdb

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

Deposited: 2024-01-08 Released: 2025-01-15
Deposition Author(s): Zhu, S.J., Bi, S.Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.260 (Depositor), 0.261 (DCC)
R-Value Work:
0.236 (Depositor), 0.237 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A complex structure of PDGFRA with an inhibitor RH140

Zhu, S.J., Bi, S.Z.

To be published.

Macromolecule Content

Total Structure Weight: 40.96 kDa
Atom Count: 2,437
Modeled Residue Count: 294
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor receptor alpha	A	356	Homo sapiens	Mutation(s): 0 EC: 2.7.10.1
UniProt
Find proteins for A0A0B4J203 (Homo sapiens) Explore A0A0B4J203 Go to UniProtKB: A0A0B4J203
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0B4J203
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LV8 (Subject of Investigation/LOI) Query on A1LV8 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]	RH140 C₂₄ H₂₅ N₅ O NUEIFXSLMFVCPQ-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: 2.57 Å
R-Value Free: 0.260 (Depositor), 0.261 (DCC)
R-Value Work: 0.236 (Depositor), 0.237 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.97	α = 90
b = 72.99	β = 90
c = 99.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	81903539

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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.