9DHH

DHODH in complex with Compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

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

Identification of isoquinolinone DHODH inhibitor isosteres.

DeRatt, L.G.Zhang, Z.Pietsch, E.C.Cisar, J.Wang, A.Wang, C.Y.Tanner, A.Shaffer, P.Jacoby, E.Kazmi, F.Shukla, N.Philippar, U.Attar, R.M.Edwards, J.P.Kuduk, S.D.

(2024) Bioorg Med Chem Lett 113: 129965-129965

  • DOI: https://doi.org/10.1016/j.bmcl.2024.129965
  • Primary Citation of Related Structures:  
    9DHG, 9DHH, 9DHI, 9DHJ

  • PubMed Abstract: 

    DHODH inhibition represents an attractive approach to overcome differentiation blockade for the treatment of AML. In a previous communication, we described our efforts leading to the discovery of compound 3 (JNJ-74856665), an orally bioavailable, potent, and selective DHODH inhibitor for clinical development. Guided by the co-crystal structures bound to human DHODH, other fused six-membered constructs were explored as isosteric replacements of the isoquinolinone central core. The correct positioning of the nitrogen in these core systems proved to be essential in modulating potency. Herein is described the synthesis of these complexly functionalized cores and their profiling, leading to DHODH inhibitors that possess favorable properties suitable for further development.


  • Organizational Affiliation

    Janssen Research and Development, Spring House, PA 19477, USA. Electronic address: lderatt@its.jnj.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial369Homo sapiensMutation(s): 0 
Gene Names: DHODH
EC: 1.3.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens)
Explore Q02127 
Go to UniProtKB:  Q02127
PHAROS:  Q02127
GTEx:  ENSG00000102967 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
A1A4O (Subject of Investigation/LOI)
Query on A1A4O

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E [auth A](3S,7P)-7-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-6-fluoro-3-(2-methylphenyl)-1-(propan-2-yl)-2,3-dihydroquinolin-4(1H)-one
C24 H27 F N4 O3
NFPQVNXNEFSIKP-GOSISDBHSA-N
LDA
Query on LDA

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U [auth A]LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
ORO
Query on ORO

Download Ideal Coordinates CCD File 
C [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4
Query on SO4

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G [auth A],
H [auth A],
O [auth A],
P [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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K [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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N [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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D [auth A]
F [auth A]
I [auth A]
M [auth A]
Q [auth A]
D [auth A],
F [auth A],
I [auth A],
M [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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J [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.813α = 90
b = 90.813β = 90
c = 122.738γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

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: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references