7JU6

Structure of RET protein tyrosine kinase in complex with selpercatinib

PDB DOI: https://doi.org/10.2210/pdb7JU6/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera aff. frugiperda 2 RZ-2014
Mutation(s): No

Deposited: 2020-08-19 Released: 2020-11-11
Deposition Author(s): Terzyan, S.S., Shen, T., Wu, J., Mooers, B.H.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.249
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of acquired resistance to selpercatinib and pralsetinib mediated by non-gatekeeper RET mutations.

Subbiah, V., Shen, T., Terzyan, S.S., Liu, X., Hu, X., Patel, K.P., Hu, M., Cabanillas, M., Behrang, A., Meric-Bernstam, F., Vo, P.T.T., Mooers, B.H.M., Wu, J.

(2021) Ann Oncol 32: 261-268

PubMed: 33161056 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.annonc.2020.10.599
Primary Citation of Related Structures:
7JU5, 7JU6

PubMed Abstract:
Selpercatinib (LOXO-292) and pralsetinib (BLU-667) are highly potent RET-selective protein tyrosine kinase inhibitors (TKIs) for treating advanced RET-altered thyroid cancers and non-small-cell lung cancer (NSCLC). It is critical to analyze RET mutants resistant to these drugs and unravel the molecular basis to improve patient outcomes.

Organizational Affiliation

Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, the University of Texas MD Anderson Cancer Center, Houston, USA. Electronic address: vsubbiah@mdanderson.org.

Macromolecule Content

Total Structure Weight: 72.7 kDa
Atom Count: 4,975
Modelled Residue Count: 579
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q6G (Subject of Investigation/LOI) Query on Q6G Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	Selpercatinib C₂₉ H₃₁ N₇ O₃ XIIOFHFUYBLOLW-ZRZAMGCNSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.249
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.621	α = 90
b = 79.975	β = 100.09
c = 79.839	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P20GM103640

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2020-11-25
Changes: Database references
Version 1.2: 2021-01-27
Changes: Database references
Version 1.3: 2023-10-18
Changes: Data collection, Database references, Refinement description