1UDT

Crystal structure of Human Phosphodiesterase 5 complexed with Sildenafil(Viagra)

Structural Biology Knowledgebase: 1UDT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1UDT

Classification: hydrolase

Total Structure Weight: 38094.86

Macromolecule Entities
Molecule Chains Length Organism Details
cGMP-specific 3',5'-cyclic phosphodiesterase A 324 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: catalytic domain
Gene Name(s): PDE5A Gene View PDE5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VIA
Query on VIA

A 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}- 1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN- 7-ONE
VIAGRA, (Synonym)
C22 H30 N6 O4 S
BNRNXUUZRGQAQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VIA EC50: 8.7 - 42 nM (100) BindingDB
IC50: 0.3 - 75 nM (95 - 100) BindingDB
Ki: 1.8 - 10 nM (95 - 100) BindingDB

Kd: 0.5 nM  BindingMOAD
Kd: 0.5 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.193
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 60.12 α = 90.00
b = 155.63 β = 90.00
c = 89.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-06
  • Released Date: 2004-05-11
  • Deposition author(s): Sung, B.-J., Lee, J.I., Heo, Y.-S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.-L., Kim, E., Eum, S.J., Lee, T.G., Cho, J.M., Park, S.-Y., Lee, J.-O., Jeon, Y.H., Hwang, K.Y., Ro, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4