8IG0

Crystal structure of menin in complex with DS-1594b

PDB DOI: https://doi.org/10.2210/pdb8IG0/pdb

Classification: TRANSCRIPTION/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-20 Released: 2023-03-22
Deposition Author(s): Suzuki, M., Yoneyama, T., Imai, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.266
R-Value Work: 0.212
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A novel Menin-MLL1 inhibitor, DS-1594a, prevents the progression of acute leukemia with rearranged MLL1 or mutated NPM1.

Numata, M., Haginoya, N., Shiroishi, M., Hirata, T., Sato-Otsubo, A., Yoshikawa, K., Takata, Y., Nagase, R., Kashimoto, Y., Suzuki, M., Schulte, N., Polier, G., Kurimoto, A., Tomoe, Y., Toyota, A., Yoneyama, T., Imai, E., Watanabe, K., Hamada, T., Kanada, R., Watanabe, J., Kagoshima, Y., Tokumaru, E., Murata, K., Baba, T., Shinozaki, T., Ohtsuka, M., Goto, K., Karibe, T., Deguchi, T., Gocho, Y., Yoshida, M., Tomizawa, D., Kato, M., Tsutsumi, S., Kitagawa, M., Abe, Y.

(2023) Cancer Cell Int 23: 36-36

PubMed: 36841758 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12935-023-02877-y
Primary Citation of Related Structures:
8IG0

PubMed Abstract:
Mixed lineage leukemia 1-rearranged (MLL1-r) acute leukemia patients respond poorly to currently available treatments and there is a need to develop more effective therapies directly disrupting the Menin‒MLL1 complex. Small-molecule-mediated inhibition of the protein‒protein interaction between Menin and MLL1 fusion proteins is a potential therapeutic strategy for patients with MLL1-r or mutated-nucleophosmin 1 (NPM1c) acute leukemia. In this study, we preclinically evaluated the new compound DS-1594a and its salts.

Organizational Affiliation

Shinagawa R&D Center, Daiichi Sankyo Co., Ltd, 1-2-5 Hiromachi, Shinagawa-Ku, Tokyo, 140-0005, Japan.

Macromolecule Content

Total Structure Weight: 247.03 kDa
Atom Count: 15,039
Modelled Residue Count: 1,944
Deposited Residue Count: 2,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menin	A, B, C, D	550	Homo sapiens	Mutation(s): 0 Gene Names: MEN1, SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens) Explore O00255 Go to UniProtKB: O00255
PHAROS: O00255 GTEx: ENSG00000133895
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00255
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7IX (Subject of Investigation/LOI) Query on 7IX Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	(1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol C₂₇ H₂₉ F₃ N₆ O₃ S FFHYBSANKGPTCW-VOQZNFBZSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]