8P5I

Kinase domain of mutant human ULK1 in complex with compound XMD-17-51

PDB DOI: https://doi.org/10.2210/pdb8P5I/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.189
R-Value Work: 0.166

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

Crystal structures of ULK1 in complex with KCGS compounds

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

To be published.

Macromolecule Content

Total Structure Weight: 130.55 kDa
Atom Count: 10,079
Modelled Residue Count: 1,082
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ULK1	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75385
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WYX (Subject of Investigation/LOI) Query on WYX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], N [auth C], R [auth D]	5,11-dimethyl-2-[(1-piperidin-4-ylpyrazol-4-yl)amino]pyrimido[4,5-b][1,4]benzodiazepin-6-one C₂₁ H₂₄ N₈ O LKOFXMLMYKWELM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	J [auth B], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain J [auth B] Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] P [auth C] F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], S [auth D], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth D]	H [auth A], M [auth B], U [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain U [auth D]