9DHJ | pdb_00009dhj

DHODH in complex with Compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.144 (Depositor), 0.153 (DCC) 
  • R-Value Work: 
    0.117 (Depositor), 0.127 (DCC) 
  • R-Value Observed: 
    0.118 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9DHJ

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 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.

Macromolecule Content 

  • Total Structure Weight: 42.66 kDa 
  • Atom Count: 3,530 
  • Modeled Residue Count: 368 
  • Deposited Residue Count: 369 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A4M
(Subject of Investigation/LOI)

Query on A1A4M



Download:Ideal Coordinates CCD File
D [auth A](2M,6P)-6-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-7-fluoro-2-(2-methylphenyl)-4-[(2R)-1,1,1-trifluoropropan-2-yl]phthalazin-1(2H)-one
C23 H21 F4 N5 O3
ATPQLRLIRAXHDW-CYBMUJFWSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ORO

Query on ORO



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

Query on PGE



Download:Ideal Coordinates CCD File
T [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
P [auth A],
Q [auth A],
R [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
G [auth A],
S [auth A],
Z [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



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],
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.144 (Depositor), 0.153 (DCC) 
  • R-Value Work:  0.117 (Depositor), 0.127 (DCC) 
  • R-Value Observed: 0.118 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.73α = 90
b = 90.73β = 90
c = 122.502γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling

Structure Validation

View Full Validation Report



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