5YAV | pdb_00005yav

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 (Depositor), 0.278 (DCC)
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 146
Deposited Residue Count: 150
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 mmCIF 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 (Depositor), 0.278 (DCC)
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.227 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.