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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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. Electronic address: david_bolduc@h3biomedicine.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthase [ammonia], mitochondrial AB1500Homo sapiensMutation(s): 0 
Gene Names: CPS1
EC: 6.3.4.16
Find proteins for P31327 (Homo sapiens)
Explore P31327 
Go to UniProtKB:  P31327
NIH Common Fund Data Resources
PHAROS:  P31327
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q5A
Query on Q5A

Download Ideal Coordinates CCD File 
A, B
N~1~-[(4-fluorophenyl)methyl]-N~1~-methyl-N~4~-(4-methyl-1,3-thiazol-2-yl)piperidine-1,4-dicarboxamide
C19 H23 F N4 O2 S
FYQIXROHNRZVMM-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references