Brand  (β version)

PDB ID: 6HWO

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Ligands
Code Name Style Show Link
EDO 1,2-ethanediol PoSSuM
PEG Di(hydroxyethyl)ether PoSSuM
ZN Zinc ion PoSSuM
FFZ 3-[5-[(4ar,8as)-4-oxidanylidene-3-propan-2-yl-4a,5,8,8a-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-N-(phenylmethyl)prop-2-ynamide PoSSuM
MG Magnesium ion PoSSuM
EPE 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid PoSSuM
Non-standard Residues
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Structure summary

Code : 6HWO   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335
Release Data : 2019-07-24
Compound :
mol_id molecule chains synonym
1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D A,B,C,D DPDE3,PDE43
ec: 3.1.4.53
other_details: residues 381-740
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: PDE4D, DPDE3
expression_system_variant: codon plus
expression_system_vector_type: Plasmid
expression_system_plasmid: pET15b
Authors : Singh, A.K., Brown, D.G.
Keywords : phosphodiesterase, hydrolase, cAMP hydrolysis, alternative splicing
Exp. method : X-RAY DIFFRACTION ( 1.99 Å )
Citation :

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2).

de Heuvel, E.,Singh, A.K.,Boronat, P.  et al.
(2019)  Bioorg.Med.Chem.  27 : 4013 - 4029

PubMed: 31378593
DOI: 10.1016/j.bmc.2019.06.026

Reaction

Chain : A, B, C, D
UniProt : Q08499 (PDE4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
3',5'-cyclic AMP + H2O = AMP + H(+) 3.1.4.53 PubMed:9371713
left-to-right
Cofactor: Evidence: Note:
Zn(2+) ECO:0000269 | PubMed:14609333
ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000269 | PubMed:17582435
Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions.
Mn(2+) ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000250 | UniProtKB:Q07343
Binds 2 divalent metal cations per subunit (PubMed:15260978, PubMed:15576036). Site 2 has a preference for magnesium and/or manganese ions (By similarity).