4UY1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.bmcl.2014.09.058

  • 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 wa ...

    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.,Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden.,Reagents and Assay Development, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden.,CVMD Innovative Medicines, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden.,Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden. Electronic address: Hongming.chen@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GROUP 10 SECRETORY PHOSPHOLIPASE A2
A, B
131Homo sapiensMutation(s): 0 
Gene Names: PLA2G10
EC: 3.1.1.4
Find proteins for O15496 (Homo sapiens)
Go to Gene View: PLA2G10
Go to UniProtKB:  O15496
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TJM
Query on TJM

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Download CCD File 
A, B
5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE
C10 H11 N3 O S
KLVHCUPVBQYXJT-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TJMIC50: 316 - 20000 nM (100) BINDINGDB
TJMIC50: 20000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.765α = 90.00
b = 86.600β = 90.00
c = 104.187γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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