5X74 | pdb_00005x74

The crystal Structure PDE delta in complex with compound (R, R)-1g

• PDB DOI: https://doi.org/10.2210/pdb5X74/pdb

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


• Deposited: 2017-02-23 Released: 2017-10-04 
• Deposition Author(s): Jiang, Y., Zhuang, C., Chen, L., Wang, R., Wang, F., Sheng, C.
• Funding Organization(s): National Basic Research Program of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural Biology-Inspired Discovery of Novel KRAS-PDE delta Inhibitors

Jiang, Y., Zhuang, C., Chen, L., Lu, J., Dong, G., Miao, Z., Zhang, W., Li, J., Sheng, C.

(2017) J Med Chem 60: 9400-9406

• PubMed: 28929751 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b01243
• Primary Citation Related Structures: 
  5X72, 5X73, 5X74


• PubMed Abstract: 
  

  Structural biology is a powerful tool for investigating the stereospecific interactions between a protein and its ligand. Herein, an unprecedented chiral binding pattern was observed for inhibitors of KRAS-PDEδ interactions. Virtual screening and X-ray crystallography studies revealed that two enantiomers of a racemic inhibitor could bind at different sites. Fragment-based drug design was used to identify highly potent PDEδ inhibitors that can be used as promising lead compounds for target validation and antitumor drug development.

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Organizational Affiliation: 
• School of Pharmacy, Second Military Medical University , Shanghai 200433, China.
School of Pharmacy, East China University of Science & Technology , Shanghai 200237, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.99 kDa 
• Atom Count: 1,317 
• Modeled Residue Count: 150 
• Deposited Residue Count: 150 
• 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	150	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JAY	B [auth A]	(2R)-2-(2-fluorophenyl)-3-[2-[4-[(2R)-2-(2-fluorophenyl)-4-oxidanylidene-1,2-dihydroquinazolin-3-yl]piperidin-1-yl]ethyl]-1,2-dihydroquinazolin-4-one C35 H33 F2 N5 O2 ZMXNWFRGUZJFLG-CZNDPXEESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JAY	BindingDB:  5X74	Kd: 2.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.7	α = 90
b = 55.7	β = 90
c = 114.902	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Jiang, Y., Zhuang, C., Chen, L., Wang, R., Wang, F., Sheng, C.

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Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2014CB541800

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description