6GQ3

Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-L-norleucine (DON) at 1.85 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity.

Zhu, W.Radadiya, A.Bisson, C.Wenzel, S.Nordin, B.E.Martinez-Marquez, F.Imasaki, T.Sedelnikova, S.E.Coricello, A.Baumann, P.Berry, A.H.Nomanbhoy, T.K.Kozarich, J.W.Jin, Y.Rice, D.W.Takagi, Y.Richards, N.G.J.

(2019) Commun Biol 2: 345-345

  • DOI: https://doi.org/10.1038/s42003-019-0587-z
  • Primary Citation of Related Structures:  
    6GQ3

  • PubMed Abstract: 

    Expression of human asparagine synthetase (ASNS) promotes metastatic progression and tumor cell invasiveness in colorectal and breast cancer, presumably by altering cellular levels of L-asparagine. Human ASNS is therefore emerging as a bona fide drug target for cancer therapy. Here we show that a slow-onset, tight binding inhibitor, which exhibits nanomolar affinity for human ASNS in vitro, exhibits excellent selectivity at 10 μM concentration in HCT-116 cell lysates with almost no off-target binding. The high-resolution (1.85 Å) crystal structure of human ASNS has enabled us to identify a cluster of negatively charged side chains in the synthetase domain that plays a key role in inhibitor binding. Comparing this structure with those of evolutionarily related AMP-forming enzymes provides insights into intermolecular interactions that give rise to the observed binding selectivity. Our findings demonstrate the feasibility of developing second generation human ASNS inhibitors as lead compounds for the discovery of drugs against metastasis.


  • Organizational Affiliation

    1School of Chemistry, Cardiff University, Cardiff, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asparagine synthetase [glutamine-hydrolyzing]
A, B
561Homo sapiensMutation(s): 0 
Gene Names: ASNSTS11
EC: 6.3.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for P08243 (Homo sapiens)
Explore P08243 
Go to UniProtKB:  P08243
GTEx:  ENSG00000070669 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08243
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ONL
Query on ONL

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
5-OXO-L-NORLEUCINE
C6 H11 N O3
KSIJECNNZVKMJG-YFKPBYRVSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 83.52β = 90.65
c = 110.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description