6FDY | pdb_00006fdy

Unc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib

PDB DOI: https://doi.org/10.2210/pdb6FDY/pdb

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

Deposited: 2017-12-27 Released: 2018-08-01
Deposition Author(s): Mathea, S., Salah, E., Moroglu, M., Scorah, A., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.239 (Depositor), 0.248 (DCC)
R-Value Work:
0.205 (Depositor), 0.217 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Unc-51-Like Kinase 3 (ULK3) In Complex With Bosutinib

Mathea, S., Salah, E., Moroglu, M., Scorah, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 33 kDa
Atom Count: 2,247
Modeled Residue Count: 262
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ULK3	A [auth U]	276	Homo sapiens	Mutation(s): 0 Gene Names: ULK3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PHR2 (Homo sapiens) Explore Q6PHR2 Go to UniProtKB: Q6PHR2
PHAROS: Q6PHR2 GTEx: ENSG00000140474
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6PHR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DB8 Query on DB8 Download:Ideal Coordinates CCD File SDF format, chain C [auth U] SDF format, chain B [auth U] MOL2 format, chain C [auth U] MOL2 format, chain B [auth U] mmCIF format, chain C [auth U] mmCIF format, chain B [auth U]	B [auth U], C [auth U]	4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile C₂₆ H₂₉ Cl₂ N₅ O₃ UBPYILGKFZZVDX-UHFFFAOYSA-N		Interactions Focus chain B [auth U] Focus chain C [auth U] Interactions & Density Focus chain B [auth U] Focus chain C [auth U]

Binding Affinity Annotations
ID	Source	Binding Affinity
DB8	BindingDB: 6FDY	Kd: 460 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.239 (Depositor), 0.248 (DCC)
R-Value Work: 0.205 (Depositor), 0.217 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.375	α = 90
b = 169.406	β = 90
c = 45.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2024-01-17
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.