5YAV

Fragment-based Drug Discovery of inhibitors to block PDEdelta-RAS protein-protein interaction

PDB DOI: https://doi.org/10.2210/pdb5YAV/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-09-01 Released: 2018-09-05
Deposition Author(s): Bing, X., Yanlian, L., Danyan, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.267
R-Value Work: 0.225
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fragment-based Drug Discovery of inhibitors to block PDEdelta-RAS protein-protein interaction

Bing, X., Yanlian, L., Danyan, C.

To be published.

Macromolecule Content

Total Structure Weight: 17.66 kDa
Atom Count: 1,300
Modelled Residue Count: 146
Deposited Residue Count: 150
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A [auth B]	150	Homo sapiens	Mutation(s): 0 Gene Names: PDE6D, PDED
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens) Explore O43924 Go to UniProtKB: O43924
PHAROS: O43924 GTEx: ENSG00000156973
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43924
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8SF (Subject of Investigation/LOI) Query on 8SF Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B	B	1-phenyl-5-propan-2-ylsulfanyl-1,2,3,4-tetrazole C₁₀ H₁₂ N₄ S SRXNAOIEUJQDHS-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.267
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.78	α = 90
b = 55.78	β = 90
c = 115.644	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHENIX	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.