9HMC | pdb_00009hmc

Crystal structure of PDE6D in complex with compound 5e

• PDB DOI: https://doi.org/10.2210/pdb9HMC/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-12-24 
• Deposition Author(s): Zhang, R., Waldmann, H., Gasper, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PDE6D in complex with compound 5e

Zhang, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38 kDa 
• Atom Count: 2,704 
• Modeled Residue Count: 297 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, B	156	Homo sapiens	Mutation(s): 0  Gene Names: PDE6D, PDED
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens) Explore O43924  Go to UniProtKB:  O43924
PHAROS:  O43924 GTEx:  ENSG00000156973

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IWC (Subject of Investigation/LOI)	C [auth A], F [auth B]	4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxidanylidene-pyrazolo[3,4-d]pyridazin-6-yl]-~{N}-heptyl-~{N}-(piperidin-4-ylmethyl)butane-1-sulfonamide C31 H48 N6 O3 S DVTXDCJEWQTSFM-UHFFFAOYSA-N
PEG	G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.74	α = 90
b = 75.65	β = 90
c = 82.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Zhang, R., Waldmann, H., Gasper, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release