7PAD: DW-0254

The crystal structure of DW-0254 in complex with PDE6D. Determined by X-ray diffraction at 1.49 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 1.49 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,476
Mol. weight: 20.16 kDa
Ligands: O7W, NI
Released: 8 Jun 2022

Explore 7PAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PAD contains 4 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 B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
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	59-67	9	1
β-strand	71-82	12	2
β-strand	85-97	13	2
β-strand	101-109	9	1
α-helix	113-116	4
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	B	protein	166	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7PAD_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains B)
MGSHHHHHHGSENLYFQSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVE
HEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNT
WQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
O7W	~{N}-[(4-ethylphenyl)methyl]-3-[5-[2-(1~{H}-indol-3-yl)ethyl]-1,3,4-oxadiazol-2…	C25 H28 N4 O2	1
NI	Nickel (II) ion	Ni	1

Water and common crystallization additives (EPE, GOL) are not listed.

Primary citation

Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects. Canovas Nunes, S., De Vita, S., Anighoro, A. et al. Blood Cancer J (2022) 12:64-64. DOI 10.1038/s41408-022-00663-z · 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
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
7Q9S 1.85 Å, Crystal structure of PDE6D KRas peptide complex with Compound-1

Browse structure collections

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