› 4jv8

X-ray diffraction
1.45Å resolution

The crystal structure of PDE6D in complex with rac-S1

Released:
DOI: 10.2210/pdb4jv8/pdb
PDB entry 4jv8 coloured by chain, front view.
PDB entry 4jv8 coloured by chain, side view.
PDB entry 4jv8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Small molecule inhibition of the KRAS-PDEδ interaction impairs oncogenic KRAS signalling.
Zimmermann G, Papke B, Ismail S, Vartak N, Chandra A, Hoffmann M, Hahn SA, Triola G, Wittinghofer A, Bastiaens PI, Waldmann H
Nature 497 638-42 (2013)
PMID: 23698361

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129171 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta Chain: B
Molecule details ›
Chain: B
Length: 152 amino acids
Theoretical weight: 17.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43924 (Residues: 1-150; Coverage: 100%)
Gene names: PDE6D, PDED
Sequence domains: GMP-PDE, delta subunit
Structure domains: GMP phosphodiesterase, delta subunit

Ligands and Environments

1 bound ligand:
Ligand 1M1 2 x 1M1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P3221
Unit cell:
a: 55.97Å b: 55.97Å c: 115.56Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.18 0.209
Expression system: Escherichia coli

Quick links

Citations

155 review citations

Drugging the undruggable RAS: Mission possible?
Cox et al. (2014)
154 more

4 mentions without citation

PDE6D Inhibitors with a New Design Principle Selectively Block K-Ras Activity.
Siddiqui et al. (2020)
3 more