6VBI

crystal structure of PDE5 in complex with a non-competitive inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6VBI/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-18 Released: 2021-01-20 
• Deposition Author(s): Ke, H., Luo, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Identification of a novel allosteric pocket and its regulation mechanism

Zhang, T., Ke, H., Luo, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.05 kDa 
• Atom Count: 5,096 
• Modelled Residue Count: 605 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A, B	325	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FZA (Subject of Investigation/LOI)	C [auth A], D [auth B]	(13bS)-4,9-dimethoxy-14-methyl-8,13,13b,14-tetrahydroindolo[2',3':3,4]pyrido[2,1-b]quinazolin-5(7H)-one C21 H21 N3 O3 FFAIVCGLKMKWII-FQEVSTJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FZA	BindingDB:  6VBI	IC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.252 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.975	α = 90
b = 85.519	β = 90
c = 124.381	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Currently 6VBI does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Ke, H., Luo, H.B.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description