1TBF

Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.157

Literature

Macromolecules
Sequence Display for 1TBF

Classification: HYDROLASE

Total Structure Weight: 40568.17

Macromolecule Entities
Molecule Chains Length Organism Details
cGMP-specific 3',5'-cyclic phosphodiesterase A 347 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: CATALYTIC DOMAIN
Mutation: R658P, N661S, S663Q, Y664F, I665L, Q666I, R667N, S668T, E669N, H670S, P671E, Q674L, L675M, C676AN, H678E, I680V, M681L
Gene Name(s): PDE5A Gene View PDE5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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 (93) BindingDB
IC50: 0.3 - 75 nM (90 - 94) BindingDB
Ki: 1.8 - 10 nM (90 - 93) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.157
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 76.10 α = 90.00
b = 76.10 β = 90.00
c = 99.27 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-20
  • Released Date: 2004-08-03
  • Deposition author(s): Zhang, K.Y.J., Card, G.L., Suzuki, Y., Artis, D.R., Fong, D., Gillette, S., Hsieh, D., Neiman, J., West, B.L., Zhang, C., Milburn, M.V., Kim, S.-H., Schlessinger, J., Bollag, G.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Non-polymer description, Version format compliance