6C7J

Crystal structure of human phosphodiesterase 2A with 1-(5-tert-butoxy-2-chloro-phenyl)-N-isobutyl-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mathematical and Structural Characterization of Strong Nonadditive Structure-Activity Relationship Caused by Protein Conformational Changes.

Gomez, L.Xu, R.Sinko, W.Selfridge, B.Vernier, W.Ly, K.Truong, R.Metz, M.Marrone, T.Sebring, K.Yan, Y.Appleton, B.Aertgeerts, K.Massari, M.E.Breitenbucher, J.G.

(2018) J. Med. Chem. 61: 7754-7766


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent 3',5'-cyclic phosphodiesterase
A, B, C, D
342Homo sapiensMutation(s): 0 
Gene Names: PDE2A
EC: 3.1.4.17
Find proteins for O00408 (Homo sapiens)
Go to Gene View: PDE2A
Go to UniProtKB:  O00408
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EPV
Query on EPV

Download SDF File 
Download CCD File 
A, B, C, D
1-(5-tert-butoxy-2-chlorophenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide
C25 H28 Cl N5 O2
NVNCEIGVCOOARY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.930α = 109.12
b = 73.450β = 91.25
c = 91.030γ = 91.56
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-01-22 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Xu, R., Aertgeerts, K.

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references
  • Version 1.2: 2018-09-26
    Type: Data collection, Database references