4WNO

Structure of ULK1 bound to an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4WNO/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-14 Released: 2015-01-14 
• Deposition Author(s): Lazarus, M.B., Novotny, C.J., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.208 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Structure of the Human Autophagy Initiating Kinase ULK1 in Complex with Potent Inhibitors.

Lazarus, M.B., Novotny, C.J., Shokat, K.M.

(2015) ACS Chem Biol 10: 257-261

• PubMed: 25551253 
• DOI: https://doi.org/10.1021/cb500835z
• Primary Citation of Related Structures:  
  4WNO, 4WNP


• PubMed Abstract: 
  

  Autophagy is a conserved cellular process that involves the degradation of cellular components for energy maintenance and cytoplasmic quality control that has recently gained interest as a novel target for a variety of human diseases, including cancer. A prime candidate to determine the potential therapeutic benefit of targeting autophagy is the kinase ULK1, whose activation initiates autophagy. Here, we report the first structures of ULK1, in complex with multiple potent inhibitors. These structures show features unique to the enzyme and will provide a path for the rational design of selective compounds as cellular probes and potential therapeutics.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,408 
• Modelled Residue Count: 273 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ULK1	A	287	Homo sapiens	Mutation(s): 2  Gene Names: ULK1, KIAA0722 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75385 (Homo sapiens) Explore O75385  Go to UniProtKB:  O75385
PHAROS:  O75385 GTEx:  ENSG00000177169

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3RF	B [auth A]	N~2~-(4-aminophenyl)-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine C20 H19 N7 CWKAMSLBSGZMJZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.208 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.78	α = 90
b = 66.78	β = 90
c = 116.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Lazarus, M.B., Novotny, C.J., Shokat, K.M.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary