4UY1

Novel pyrazole series of group X Secretory Phospholipase A2 (sPLA2-X) inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of a Novel Pyrazole Series of Group X Secreted Phospholipase A2 Inhibitor (Spla2X) Via Fragment Based Virtual Screening

Chen, H.Knerr, L.Akerud, T.Hallberg, K.Bodin, C.Oster, L.Rohman, M.Osterlund, K.Beisel, H.G.Olsson, T.Brengdhal, J.Sandmark, J.

(2014) Bioorg Med Chem Lett 24: 5251

  • DOI: https://doi.org/10.1016/j.bmcl.2014.09.058
  • Primary Citation of Related Structures:  
    4UY1

  • PubMed Abstract: 

    The discovery of potent novel pyrazole containing group X secreted phospholipase A2 inhibitors via structure based virtual screening is reported. Docking was applied on a large set of in-house fragment collection and pharmacophore feature matching was used to filter docking poses. The selected virtual screening hits was run in NMR screening, a potent pyrazole containing fragment hit was identified and confirmed by its complex X-ray structure and the following biochemical assay result. Expansion on the fragment hit has led to further improvement of potency while maintaining high ligand efficiency, thus supporting the further development of this chemical series.


  • Organizational Affiliation

    Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden. Electronic address: Hongming.chen@astrazeneca.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GROUP 10 SECRETORY PHOSPHOLIPASE A2
A, B
131Homo sapiensMutation(s): 0 
EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for O15496 (Homo sapiens)
Explore O15496 
Go to UniProtKB:  O15496
PHAROS:  O15496
GTEx:  ENSG00000069764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15496
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
O [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
TJM
Query on TJM

Download Ideal Coordinates CCD File 
J [auth A],
S [auth B]
5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE
C10 H11 N3 O S
KLVHCUPVBQYXJT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
T [auth B]
U [auth B]
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B],
V [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TJM BindingDB:  4UY1 IC50: min: 316, max: 2.00e+4 (nM) from 2 assay(s)
Binding MOAD:  4UY1 IC50: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.765α = 90
b = 86.6β = 90
c = 104.187γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2018-04-04
    Changes: Data collection