Zinc in PDB 6kk0: Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E

All present enzymatic activity of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E:
3.1.4.53;

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E, PDB code: 6kk0 was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.93 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.365, 77.984, 163.344, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E (pdb code 6kk0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E, PDB code: 6kk0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:23.5 occ:1.00 O37 A:M36501 2.0 21.8 1.0 O A:HOH657 2.1 49.8 1.0 OD1 A:ASP318 2.2 14.7 1.0 OD2 A:ASP201 2.2 17.2 1.0 NE2 A:HIS164 2.2 13.5 1.0 NE2 A:HIS200 2.3 12.4 1.0 CG A:ASP318 3.0 19.4 1.0 CD2 A:HIS200 3.0 18.1 1.0 CD2 A:HIS164 3.1 15.5 1.0 C35 A:M36501 3.1 23.0 1.0 CG A:ASP201 3.2 16.6 1.0 OD2 A:ASP318 3.2 24.2 1.0 CE1 A:HIS164 3.2 13.7 1.0 MG A:MG503 3.5 19.4 1.0 CE1 A:HIS200 3.5 16.5 1.0 OD1 A:ASP201 3.6 16.7 1.0 C34 A:M36501 3.9 20.8 1.0 O A:HOH702 4.0 20.8 1.0 O36 A:M36501 4.1 23.9 1.0 CG A:HIS164 4.3 18.7 1.0 CG A:HIS200 4.3 14.5 1.0 ND1 A:HIS164 4.3 15.4 1.0 CD2 A:HIS160 4.3 15.0 1.0 CB A:ASP201 4.4 19.6 1.0 CB A:ASP318 4.4 18.7 1.0 ND1 A:HIS200 4.5 13.9 1.0 CG2 A:VAL168 4.8 11.2 1.0 NE2 A:HIS160 4.8 17.2 1.0 O A:HOH663 4.8 18.7 1.0 CA A:ASP318 5.0 17.2 1.0

Zinc binding site 2 out of 2 in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:22.5 occ:1.00 O37 B:M36501 2.1 21.6 1.0 OD1 B:ASP318 2.1 14.2 1.0 O B:HOH641 2.1 18.2 1.0 NE2 B:HIS200 2.1 19.2 1.0 OD2 B:ASP201 2.2 17.7 1.0 NE2 B:HIS164 2.3 17.4 1.0 CD2 B:HIS200 2.9 16.4 1.0 CG B:ASP318 2.9 20.9 1.0 OD2 B:ASP318 3.1 25.7 1.0 CD2 B:HIS164 3.1 20.4 1.0 CG B:ASP201 3.2 25.7 1.0 C35 B:M36501 3.2 22.6 1.0 CE1 B:HIS200 3.3 21.1 1.0 CE1 B:HIS164 3.4 20.7 1.0 MG B:MG503 3.7 14.5 1.0 OD1 B:ASP201 3.7 16.6 1.0 O B:HOH672 4.0 16.2 1.0 C34 B:M36501 4.0 22.7 1.0 CG B:HIS200 4.2 15.8 1.0 O36 B:M36501 4.2 26.3 1.0 ND1 B:HIS200 4.3 19.0 1.0 CD2 B:HIS160 4.3 19.4 1.0 CG B:HIS164 4.3 21.6 1.0 CB B:ASP318 4.4 19.3 1.0 ND1 B:HIS164 4.4 17.1 1.0 CB B:ASP201 4.4 17.8 1.0 O B:HOH633 4.7 16.5 1.0 NE2 B:HIS160 4.8 20.3 1.0 CG2 B:VAL168 4.8 15.3 1.0 CA B:ASP318 5.0 19.3 1.0

J.Liang, Y.Y.Huang, Q.Zhou, Y.Gao, Z.Li, D.Wu, S.Yu, L.Guo, Z.Chen, L.Huang, S.H.Liang, X.He, R.Wu, H.B.Luo. Discovery and Optimization of Alpha-Mangostin Derivatives As Novel PDE4 Inhibitors For the Treatment of Vascular Dementia. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32115956
DOI: 10.1021/ACS.JMEDCHEM.0C00060