8UOH | pdb_00008uoh

Crystal structure of human NUAK1-MARK3 kinase domain chimera bound with small molecule inhibitor #10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of UCB9386: A Potent, Selective, and Brain-Penetrant Nuak1 Inhibitor Suitable for In Vivo Pharmacological Studies.

Poullennec, K.G.Jnoff, E.Abendroth, J.Bhuma, N.Calmiano, M.Calmus, L.Cardenas, A.Courade, J.P.Delatour, C.Hall, A.de Haro, T.Delker, S.L.Demaude, T.Gaikwad, N.Ghavate, D.Gholap, A.R.Kierkowicz, M.Le Mestre, R.Van Hijfte, N.Verheijden, S.Vernerova, K.De Wever, V.Waghmode, N.

(2024) J Med Chem 67: 20879-20910

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01237
  • Primary Citation of Related Structures:  
    8UOH, 8UOI, 8UOJ, 8UOK, 8UOL

  • PubMed Abstract: 

    Nuak1 (NUAK family SnF1-like kinase-1) is a serine-threonine kinase and a member of the AMPK family. Interest in Nuak1 has increased over the years due to the role it plays in several biological processes, from tumor cell invasion and proliferation to Tau stabilization. Nuak1 is expressed in many cancer cell lines and many reports describe this target as an oncogene, the inhibition of which is hypothesized to be valuable for treating various cancer types including glioma. We report here the discovery of Nuak1 inhibitors originating from HTS hit 9 with excellent selectivity and the subsequent medicinal chemistry optimization program, supported by structural information from the first crystal structures of a Nuak1 chimeric protein which provided insights into the binding modes of our compounds. These efforts yielded a nanomolar cell potent, highly selective and brain penetrant Nuak1 inhibitor UCB9386 ( 56 ) suitable for in vivo pharmacological studies for central nervous system (CNS) disorders.


  • Organizational Affiliation
    • Chemin du Foriest, UCB, 1420 Braine l'Alleud, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP/microtubule affinity-regulating kinase 3
A, B
328Homo sapiensMutation(s): 6 
Gene Names: MARK3CTAK1EMK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P27448 (Homo sapiens)
Explore P27448 
Go to UniProtKB:  P27448
PHAROS:  P27448
GTEx:  ENSG00000075413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27448
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X4W (Subject of Investigation/LOI)
Query on X4W

Download Ideal Coordinates CCD File 
G [auth B](6P)-6-[(4S)-imidazo[1,2-a]pyridin-3-yl]-4-[(1R)-1-phenylethyl]-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one
C22 H18 N4 O2
SYVMVOGMTMPBEH-OAHLLOKOSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
F [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.88α = 90
b = 113.41β = 90
c = 116.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

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: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references