9MFP | pdb_00009mfp

Cat DHX9 in Complex with Compound 1 and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of ATX968: An Orally Available Allosteric Inhibitor of DHX9.

Daniels, M.H.Castro, J.Lee, Y.T.Gotur, D.Knockenhauer, K.E.Grigoriu, S.Lockbaum, G.J.Cheong, J.E.Lu, C.Brennan, D.Buker, S.M.Liu, J.Yao, S.Sparling, B.A.Sickmier, E.A.Ribich, S.Blakemore, S.J.Silver, S.J.Boriack-Sjodin, P.A.Duncan, K.W.Copeland, R.A.

(2025) J Med Chem 68: 9537-9554

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00252
  • Primary Citation of Related Structures:  
    9MFO, 9MFP, 9MFQ, 9MFR, 9MFS, 9MFT

  • PubMed Abstract: 

    DHX9 is an RNA/DNA helicase integral in the maintenance of genome stability that has emerged as an attractive target for oncology drug discovery. Disclosed herein is the discovery and optimization of a series of DHX9 inhibitors. Compound 1 was identified as a partial inhibitor of DHX9 ATPase activity but a full inhibitor of unwinding activity. Binding of 1 to a pocket distinct from the ATP binding site was confirmed by X-ray crystallography, enabling structure-based drug optimization. During this optimization, a sulfur-halogen bond was identified that increased on-target residence time without impacting equilibrium binding affinity. Analysis shows that cell potency more closely correlates with residence time than with equilibrium measurements of binding affinity or biochemical potency. Further optimization of potency and ADME properties led to the identification of ATX968 , a potent and selective DHX9 inhibitor that is efficacious in a tumor xenograft model of microsatellite instability-high (MSI-H) colorectal cancer.


  • Organizational Affiliation
    • Accent Therapeutics, Inc., 1050 Waltham Street, Lexington, Massachusetts 02421, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicase1,010Felis catusMutation(s): 0 
Gene Names: DHX9
EC: 3.6.4.13
UniProt
Find proteins for M3WPI7 (Felis catus)
Explore M3WPI7 
Go to UniProtKB:  M3WPI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM3WPI7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1BK0 (Subject of Investigation/LOI)
Query on A1BK0

Download Ideal Coordinates CCD File 
B [auth A]1-ethyl-N-[3-(methanesulfonamido)phenyl]-5-methyl-1H-pyrazole-3-carboxamide
C14 H18 N4 O3 S
RNCRRFDHODBLRY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.47α = 90
b = 86.47β = 90
c = 351.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
XDSdata scaling
PHASERphasing
Cootmodel building
Aimlessdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references