8P5L | pdb_00008p5l

Kinase domain of mutant human ULK1 in complex with compound MRT67307

• PDB DOI: https://doi.org/10.2210/pdb8P5L/pdb

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


• Deposited: 2023-05-24 Released: 2024-06-05 
• Deposition Author(s): Battista, T., Semrau, M.S., Heroux, A., Lolli, G., Storici, P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structures of ULK1 in complex with KCGS compounds

Battista, T., Semrau, M.S., Lolli, G., Storici, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.27 kDa 
• Atom Count: 4,952 
• Modeled Residue Count: 538 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ULK1	A, B	284	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FV (Subject of Investigation/LOI)	C [auth A], F [auth B]	N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide C26 H36 N6 O2 UKBGBACORPRCGG-UHFFFAOYSA-N
MG	D [auth A], E [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
1FV	BindingDB:  8P5L	IC50: min: 2.9, max: 170 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.6	α = 90
b = 152.6	β = 90
c = 206.14	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Battista, T., Semrau, M.S., Heroux, A., Lolli, G., Storici, P.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary