8YLC | pdb_00008ylc

The crystal structure of PDE4D with Amentoflavone

PDB DOI: https://doi.org/10.2210/pdb8YLC/pdb

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

Deposited: 2024-03-06 Released: 2024-06-12
Deposition Author(s): Huang, Y.-Y., Luo, H.-B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.258 (Depositor), 0.268 (DCC)
R-Value Work:
0.214 (Depositor), 0.221 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of amentoflavone as a natural PDE4 inhibitor with anti-fibrotic effects

Chen, Z., Shi, Y., Zhong, F., Zhang, K., Zhang, F., Xie, S., Cheng, Z., Zhou, Q., Huang, Y.Y., Luo, H.B.

(2024) Chin Chem Lett : 109956

DOI: https://doi.org/10.1016/j.cclet.2024.109956

Macromolecule Content

Total Structure Weight: 116.77 kDa
Atom Count: 5,477
Modeled Residue Count: 649
Deposited Residue Count: 1,012
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3',5'-cyclic-AMP phosphodiesterase 4D	A, B	506	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
A1D6Q (Subject of Investigation/LOI) Query on A1D6Q 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]	8-[5-[5,7-bis(oxidanyl)-4-oxidanylidene-chromen-2-yl]-2-oxidanyl-phenyl]-2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)chromen-4-one C₃₀ H₁₈ O₁₀ YUSWMAULDXZHPY-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]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-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]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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]