6KZE | pdb_00006kze

The crystal structue of PDE10A complexed with 4d

• PDB DOI: https://doi.org/10.2210/pdb6KZE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-09-24 Released: 2020-09-30 
• Deposition Author(s): Yang, Y., Zhang, S., Zhou, Q., Huang, Y.-Y., Guo, L., Luo, H.-B.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.328 (Depositor), 0.328 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Novel Potent and Highly Selective Benzoimidazole-based Phosphodiesterase 10 Inhibitors with Improved Solubility and Pharmacokinetic Properties for the Treatment of Pulmonary Arterial Hypertension

Yang, Y., Zhang, S., Zhou, Q., Huang, Y.-Y., Huang, J., Li, Z., Gao, Y., Wu, Y., Wu, D., Luo, H.-B., Guo, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.79 kDa 
• Atom Count: 5,236 
• Modeled Residue Count: 625 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	322	Homo sapiens	Mutation(s): 0  Gene Names: PDE10A EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens) Explore Q9Y233  Go to UniProtKB:  Q9Y233
PHAROS:  Q9Y233 GTEx:  ENSG00000112541

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DZU (Subject of Investigation/LOI)	C [auth A], F [auth B]	8-[(E)-2-[5-methyl-1-[3-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]benzimidazol-2-yl]ethenyl]quinoline C33 H35 N5 O KQVBPBWJTADBHJ-FYWRMAATSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.328 (Depositor), 0.328 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.495	α = 90
b = 81.147	β = 90
c = 162.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Yang, Y., Zhang, S., Zhou, Q., Huang, Y.-Y., Guo, L., Luo, H.-B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21572279
National Natural Science Foundation of China	China	21708052
National Natural Science Foundation of China	China	21877134
National Natural Science Foundation of China	China	81602955
National Natural Science Foundation of China	China	81703341

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description