7BTT | pdb_00007btt

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 (Depositor), 0.212 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 304
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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]

Binding Affinity Annotations
ID	Source	Binding Affinity
F8R	BindingDB: 7BTT	IC50: 4.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.209 (Depositor), 0.212 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.