9RP6: PDB entry 9RP6

Crystal structure of covalent PDE6delta adduct modified by compound 13b. Determined by X-ray diffraction at 1.8 Å resolution. Released 29 Apr 2026.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,346
Mol. weight: 18.98 kDa
Ligands: A1JIC
Released: 29 Apr 2026

Explore 9RP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RP6 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 A: 4 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	45-49	5	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	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	A	protein	156	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9RP6_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains A)
HHHHHHMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKIL
KCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPE
SQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
A1JIC	4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxidanylidene-pyrazolo[3,4-d]pyridazin-6-y…	C33 H45 N7 O3 S	1

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

Primary citation

Targeting a Glutamic Acid in PDE delta with Fluoromethyl-Aryl Electrophiles Impairs K-Ras Signaling. Zhang, R., Huetzen, M.A., Binici, A. et al. J Med Chem (2026) 69:964-981. DOI 10.1021/acs.jmedchem.5c02082 · 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)
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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