8IG0

Crystal structure of menin in complex with DS-1594b

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


This is version 1.0 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

  • 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MeninA, B, C, D550Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00255
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7IX (Subject of Investigation/LOI)
Query on 7IX
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
UNX
Query on UNX
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]		UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.576α = 90
b = 70.151β = 91.47
c = 144.426γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release