6W2J

CPS1 bound to allosteric inhibitor H3B-374


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Discovery of 2,6-Dimethylpiperazines as Allosteric Inhibitors of CPS1.

Rolfe, A.Yao, S.Nguyen, T.V.Omoto, K.Colombo, F.Virrankoski, M.Vaillancourt, F.H.Yu, L.Cook, A.Reynolds, D.Ioannidis, S.Zhu, P.Larsen, N.A.Bolduc, D.M.

(2020) ACS Med Chem Lett 11: 1305-1309

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00145
  • Primary Citation of Related Structures:  
    6W2J

  • PubMed Abstract: 

    Carbamoyl phosphate synthetase 1 (CPS1) is a potential synthetic lethal target in LKB1-deficient nonsmall cell lung cancer, where its overexpression supports the production of pyrimidine synthesis. In other cancer types, CPS1 overexpression and activity may prevent the accumulation of toxic levels of intratumoral ammonia to support tumor growth. Herein we report the discovery of a novel series of potent and selective small-molecule inhibitors of CPS1. Piperazine 2 was initially identified as a promising CPS1 inhibitor through a high-throughput screening effort. Subsequent structure-activity relationship optimization and structure-based drug design led to the discovery of piperazine H3B-616 ( 25 ), a potent allosteric inhibitor of CPS1 (IC 50 = 66 nM).


  • Organizational Affiliation

    H3 Biomedicine Inc., 300 Technology Square, Fifth Floor, Cambridge, Massachusetts 02139, United States.


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: 2.62 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.66α = 102.13
b = 98.53β = 97.94
c = 142.53γ = 106.11
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata 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: 2021-01-13
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description