6KK0 | pdb_00006kk0

Crystal structure of PDE4D catalytic domain complexed with compound 4e

PDB DOI: https://doi.org/10.2210/pdb6KK0/pdb

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

Deposited: 2019-07-23 Released: 2020-03-18
Deposition Author(s): Huang, Y.-Y., He, X., Luo, H.-B.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery and Optimization of alpha-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia.

Liang, J., Huang, Y.Y., Zhou, Q., Gao, Y., Li, Z., Wu, D., Yu, S., Guo, L., Chen, Z., Huang, L., Liang, S.H., He, X., Wu, R., Luo, H.B.

(2020) J Med Chem 63: 3370-3380

PubMed: 32115956 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.0c00060
Primary Citation Related Structures:
6KJZ, 6KK0

PubMed Abstract:
To validate PDE4 inhibitors as novel therapeutic agents against vascular dementia (VaD), 25 derivatives were discovered from the natural inhibitor α-mangostin (IC ₅₀ = 1.31 μM). Hit-to-lead optimization identified a novel and selective PDE4 inhibitor 4e (IC ₅₀ = 17 nM), which adopted a different binding pattern from PDE4 inhibitors roflumilast and rolipram. Oral administration of 4e at a dose of 10 mg/kg exhibited remarkable therapeutic effects in a VaD model and did not cause emesis to beagle dogs, indicating its potential as a novel anti-VaD agent.

Organizational Affiliation

School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China.

Macromolecule Content

Total Structure Weight: 76.41 kDa
Atom Count: 5,634
Modeled Residue Count: 649
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B	326	Homo sapiens	Mutation(s): 0 Gene Names: PDE4D, DPDE3 EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499 Go to UniProtKB: Q08499
PHAROS: Q08499 GTEx: ENSG00000113448
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08499
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M36 (Subject of Investigation/LOI) Query on M36 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	7-[8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-5-oxidanyl-6-oxidanylidene-pyrano[3,2-b]xanthen-9-yl]oxyheptanoic acid C₃₁ H₃₆ O₈ QHLZYKWHQKCZMD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247 (Depositor), 0.249 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.365	α = 90
b = 77.984	β = 90
c = 163.344	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Huang, Y.-Y.

He, X.

Luo, H.-B.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21877134
National Natural Science Foundation of China	China	81522041
National Natural Science Foundation of China	China	21572279

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2020-04-08
Changes: Database references
Version 1.2: 2020-05-13
Changes: Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description