9F9A

Crystal structure of MUS81-EME1 bound by compound 12.

PDB DOI: https://doi.org/10.2210/pdb9F9A/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-05-07 Released: 2024-06-19
Deposition Author(s): Collie, G.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.278
R-Value Work: 0.243
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Fragment-Based Discovery of Novel MUS81 Inhibitors

Collie, G.W., Borjesson, U., Chen, Y., Dong, Z., Di Fruscia, P., Gohlke, A., Hoyle, A., Hunt, T.A., Jesani, M.H., Luo, H., Luptak, J., Milbradt, A.G., Narasimhan, P., Packer, M., Patel, S., Qiao, J., Storer, R.I., Stubbs, C.J., Tart, J., Truman, C., Wang, A.T., Wheeler, M.G., Winter-Holt, J.

(2024) ACS Med Chem Lett

DOI: https://doi.org/10.1021/acsmedchemlett.3c00453

Macromolecule Content

Total Structure Weight: 282.54 kDa
Atom Count: 10,093
Modelled Residue Count: 1,296
Deposited Residue Count: 2,536
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Crossover junction endonuclease MUS81	A, C, E, G	308	Homo sapiens	Mutation(s): 0 Gene Names: MUS81 EC: 3.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NY9 (Homo sapiens) Explore Q96NY9 Go to UniProtKB: Q96NY9
PHAROS: Q96NY9 GTEx: ENSG00000172732
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96NY9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Crossover junction endonuclease EME1	B, D, F, H	326	Homo sapiens	Mutation(s): 0 Gene Names: EME1, MMS4 EC: 3.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AY2 (Homo sapiens) Explore Q96AY2 Go to UniProtKB: Q96AY2
PHAROS: Q96AY2 GTEx: ENSG00000154920
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96AY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IA6 (Subject of Investigation/LOI) Query on A1IA6 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain O [auth E] SDF format, chain R [auth G] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth E] MOL2 format, chain R [auth G]	I [auth A], L [auth C], O [auth E], R [auth G]	2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid C₁₅ H₁₀ N₂ O₄ HQQIELXMZFSTOA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain S [auth G] SDF format, chain T [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G]	J [auth A] K [auth A] M [auth C] N [auth C] P [auth E] J [auth A], K [auth A], M [auth C], N [auth C], P [auth E], Q [auth E], S [auth G], T [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth G] Focus chain T [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth G] Focus chain T [auth G]