6I82 | pdb_00006i82

Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018412

PDB DOI: https://doi.org/10.2210/pdb6I82/pdb

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

Deposited: 2018-11-19 Released: 2020-03-11
Deposition Author(s): Burschowsky, D., Seewooruthun, C., Bayliss, R., Carr, M.D., Echalier, A., Jordan, A.M.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery and Optimization of wt-RET/KDR-Selective Inhibitors of RETV804MKinase.

Newton, R., Waszkowycz, B., Seewooruthun, C., Burschowsky, D., Richards, M., Hitchin, S., Begum, H., Watson, A., French, E., Hamilton, N., Jones, S., Lin, L.Y., Waddell, I., Echalier, A., Bayliss, R., Jordan, A.M., Ogilvie, D.

(2020) ACS Med Chem Lett 11: 497-505

PubMed: 32292556 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.9b00615
Primary Citation of Related Structures:
6I82, 6I83

PubMed Abstract:
A combination of focused library and virtual screening, hit expansion, and rational design has resulted in the development of a series of inhibitors of RET ^V804M kinase, the anticipated drug-resistant mutant of RET kinase. These agents do not inhibit the wild type (wt) isoforms of RET or KDR and therefore offer a potential adjunct to RET inhibitors currently undergoing clinical evaluation.

Organizational Affiliation

Drug Discovery Unit, Cancer Research UK, Manchester Institute, University of Manchester, Alderley Park, Macclesfield SK10 4TG, U.K.

Macromolecule Content

Total Structure Weight: 73.36 kDa
Atom Count: 4,897
Modelled Residue Count: 567
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): 1 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 LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H6W (Subject of Investigation/LOI) Query on H6W Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	~{N}-[3-(1,3-benzodioxol-5-yl)pyrazolo[1,5-a]pyrimidin-5-yl]-~{N}',~{N}'-dimethyl-propane-1,3-diamine C₁₈ H₂₁ N₅ O₂ DQYRQFLRDJTHQM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	D [auth A], E [auth A], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
H6W	BindingDB: 6I82	IC50: min: 19, max: 4000 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.675	α = 90
b = 80.336	β = 99.87
c = 79.74	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	Grant C480/A11411
Cancer Research UK	United Kingdom	C5759/A17098
Cancer Research UK	United Kingdom	C1362/A20263

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2020-04-22
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary