5ML3: PDE6D in complex to Deltasonamide1

The crystal structure of PDE6D in complex to Deltasonamide1. Determined by X-ray diffraction at 1.4 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,447
Mol. weight: 17.96 kDa
Ligands: DL3
Released: 1 Feb 2017

Explore 5ML3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ML3 contains 5 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: 5 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	111-112	2
α-helix	117-119	3
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	149	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5ML3_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains B)
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSR
ELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPAS
VLTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
DL3	~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimid…	C30 H39 Cl N6 O4 S2	1

Primary citation

A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Martin-Gago, P., Fansa, E.K., Klein, C.H. et al. Angew Chem Int Ed Engl (2017) 56:2423-2428. DOI 10.1002/anie.201610957 · PubMed

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

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
7Q9S 1.85 Å, Crystal structure of PDE6D KRas peptide complex with Compound-1

Browse structure collections

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