7DU9 | pdb_00007du9

Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with Pralsetinib

PDB DOI: https://doi.org/10.2210/pdb7DU9/pdb

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

Deposited: 2021-01-08 Released: 2022-01-12
Deposition Author(s): Miyazaki, I., Ishida, K., Suzuki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.249 (Depositor), 0.240 (DCC)
R-Value Work:
0.219 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Selective RET inhibitor TAS0953/HM06

Miyazaki, I., Ishida, K., Suzuki, T.

To be published.

Macromolecule Content

Total Structure Weight: 72.48 kDa
Atom Count: 4,736
Modeled Residue Count: 558
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase receptor Ret	A, B	314	Homo sapiens	Mutation(s): 0 Gene Names: RET, CDHF12, CDHR16, PTC, RET51 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens) Explore P07949 Go to UniProtKB: P07949
PHAROS: P07949 GTEx: ENSG00000165731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07949
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q4J (Subject of Investigation/LOI) Query on Q4J Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	Pralsetinib C₂₇ H₃₂ F N₉ O₂ GBLBJPZSROAGMF-BATDWUPUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
Q4J	BindingDB: 7DU9	Kd: 1 (nM) from 1 assay(s)
Q4J	BindingDB: 7DU9	IC50: min: 100, max: 6000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.249 (Depositor), 0.240 (DCC)
R-Value Work: 0.219 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.887	α = 90
b = 80.577	β = 99.72
c = 79.866	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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.