6UEL

CPS1 bound to allosteric inhibitor H3B-193


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Small Molecule Inhibition of CPS1 Activity through an Allosteric Pocket.

Yao, S.Nguyen, T.V.Rolfe, A.Agrawal, A.A.Ke, J.Peng, S.Colombo, F.Yu, S.Bouchard, P.Wu, J.Huang, K.C.Bao, X.Omoto, K.Selvaraj, A.Yu, L.Ioannidis, S.Vaillancourt, F.H.Zhu, P.Larsen, N.A.Bolduc, D.M.

(2020) Cell Chem Biol 27: 259-268.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2020.01.009
  • Primary Citation of Related Structures:  
    6UEL

  • PubMed Abstract: 

    Carbamoyl phosphate synthetase 1 (CPS1) catalyzes the first step in the ammonia-detoxifying urea cycle, converting ammonia to carbamoyl phosphate under physiologic conditions. In cancer, CPS1 overexpression supports pyrimidine synthesis to promote tumor growth in some cancer types, while in others CPS1 activity prevents the buildup of toxic levels of intratumoral ammonia to allow for sustained tumor growth. Targeted CPS1 inhibitors may, therefore, provide a therapeutic benefit for cancer patients with tumors overexpressing CPS1. Herein, we describe the discovery of small-molecule CPS1 inhibitors that bind to a previously unknown allosteric pocket to block ATP hydrolysis in the first step of carbamoyl phosphate synthesis. CPS1 inhibitors are active in cellular assays, blocking both urea synthesis and CPS1 support of the pyrimidine biosynthetic pathway, while having no activity against CPS2. These newly discovered CPS1 inhibitors are a first step toward providing researchers with valuable tools for probing CPS1 cancer biology.


  • Organizational Affiliation

    H3 Biomedicine Inc., 300 Technology Square, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthase [ammonia], mitochondrial
A, B
1,500Homo sapiensMutation(s): 0 
Gene Names: CPS1
EC: 6.3.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P31327 (Homo sapiens)
Explore P31327 
Go to UniProtKB:  P31327
PHAROS:  P31327
GTEx:  ENSG00000021826 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31327
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.587α = 90
b = 132.342β = 102.57
c = 142.443γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description