6ACB | pdb_00006acb

Crystal structure of PDE5 in complex with inhibitor LW1805


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6ACB

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Optimization of Chromeno[2,3- c]pyrrol-9(2 H)-ones as Highly Potent, Selective, and Orally Bioavailable PDE5 Inhibitors: Structure-Activity Relationship, X-ray Crystal Structure, and Pharmacodynamic Effect on Pulmonary Arterial Hypertension.

Wu, D.Huang, Y.Chen, Y.Huang, Y.Y.Geng, H.Zhang, T.Zhang, C.Li, Z.Guo, L.Chen, J.Luo, H.B.

(2018) J Med Chem 61: 8468-8473

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01209
  • Primary Citation Related Structures: 
    5ZZ2, 6ACB

  • PubMed Abstract: 

    To further explore the structure-activity relationship around the chromeno[2,3- c]pyrrol-9(2 H)-one scaffold, 19 derivatives as inhibitors against PDE5 were discovered. The most potent inhibitor 3 has an IC 50 of 0.32 nM with remarkable selectivity and druglike profile. Oral administration of 3 (1.25 mg/kg) caused comparable therapeutic effects to sildenafil (10.0 mg/kg) against pulmonary arterial hypertension. Further, different binding patterns from sildenafil were revealed in cocrystal structures, which provide structural templates for discovery of highly potent PDE5 inhibitors.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P. R. China.

Macromolecule Content 

  • Total Structure Weight: 38.54 kDa 
  • Atom Count: 2,591 
  • Modeled Residue Count: 308 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase326Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
GTEx:  ENSG00000138735 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.577α = 90
b = 74.577β = 90
c = 132.092γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81602955
National Natural Science Foundation of ChinaChina21702238

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary