7BTT

A X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain

PDB DOI: https://doi.org/10.2210/pdb7BTT/pdb

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

Deposited: 2020-04-02 Released: 2021-04-07
Deposition Author(s): Yun, C.H., Zhu, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.209
R-Value Work: 0.187
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain

Yun, C.H., Zhu, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 36.5 kDa
Atom Count: 2,588
Modelled Residue Count: 304
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	320	Homo sapiens	Mutation(s): 0 Gene Names: ALK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens) Explore Q9UM73 Go to UniProtKB: Q9UM73
PHAROS: Q9UM73 GTEx: ENSG00000171094
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UM73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F8R (Subject of Investigation/LOI) Query on F8R 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]	2-(dimethylamino)-1-[5-methoxy-6-[[4-[(2-propan-2-ylsulfonylphenyl)amino]-5H-pyrrolo[3,2-d]pyrimidin-2-yl]amino]-2,3-dihydroindol-1-yl]ethanone C₂₈ H₃₃ N₇ O₄ S HTWIYZGXLMTRHE-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: 1.86 Å
R-Value Free: 0.209
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.525	α = 90
b = 57.441	β = 90
c = 105.404	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2023-11-29
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.