6C7I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.713 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 

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
EP7
Query on EP7

Download SDF File 
Download CCD File 
A, B, C, D
1-(2-chloro-5-methoxyphenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide
C22 H22 Cl N5 O2
FAIPSSKYXVXTPM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.713 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.902α = 109.33
b = 72.682β = 91.13
c = 90.816γ = 91.06
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
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