5X72: The crystal Structure PDE delta

The crystal Structure PDE delta in complex with (rac)-p9. Determined by X-ray diffraction at 1.95 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,354
Mol. weight: 18.08 kDa
Ligands: P59, P69
Released: 4 Oct 2017

Explore 5X72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X72 contains 3 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	15-24	10	1
β-strand	30-34	5	1
β-strand	44-49	6	2
α-helix	51-55	5
β-strand	58-67	10	1
β-strand	71-82	12	2
β-strand	85-97	13	2
β-strand	101-110	10	1
α-helix	120-123	4
β-strand	127-135	9	2
β-strand	138-149	12	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A	protein	150	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5X72_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains A)
MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVS
RELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPA
SVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
P59	(2R)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one	C20 H15 F N2 O	1
P69	(2S)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one	C20 H15 F N2 O	1

Primary citation

Structural Biology-Inspired Discovery of Novel KRAS-PDE delta Inhibitors. Jiang, Y., Zhuang, C., Chen, L. et al. J Med Chem (2017) 60:9400-9406. DOI 10.1021/acs.jmedchem.7b01243 · PubMed

Other PDB entries of the same protein (UniProt O43924 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ML3 1.4 Å, The crystal structure of PDE6D in complex to Deltasonamide1
4JV8 1.45 Å, The crystal structure of PDE6D in complex with rac-S1
7Q9Q 1.45 Å, Crystal structure of PDE6D Geranylgeranylated cystein complex
7PAD 1.49 Å, The crystal structure of DW-0254 in complex with PDE6D
5ML2 1.6 Å, The crystal structure of PDE6D in complex with inhibitor-3
9HMC 1.65 Å, Crystal structure of PDE6D in complex with compound 5e
3T5G 1.7 Å, Structure of fully modified farnesylated Rheb in complex with PDE6D
4JVB 1.75 Å, Crystal structure of PDE6D in complex with the inhibitor rac-2
1KSH 1.8 Å, Complex of Arl2 and PDE delta, Crystal Form 2 (native)
9RP6 1.8 Å, Crystal structure of covalent PDE6delta adduct modified by compound 13b
5F2U 1.85 Å, Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D
7PAE 1.85 Å, The crystal structure of Deltarasin in complex with PDE6D

Browse structure collections

About this viewer

MolViewer shows 5X72 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.