6IBF: Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417

PDB ID: 6IBFDownload
MMDB ID: 182292
PDB Deposition Date: 2018/11/29
Updated in MMDB: 2019/12
Experimental Method:
x-ray diffraction
Resolution: 2.31  Å
Source Organism:
Similar Structures:
Biological Unit for 6IBF: monomeric; determined by author
Molecular Components in 6IBF
Label Count Molecule
Protein (1 molecule)
1
Camp-specific 3',5'-cyclic Phosphodiesterase 4D
(Gene symbol: PDE4D)
Molecule annotation
Chemicals and Non-standard biopolymers (16 molecules)
1
1
ZINC IONZINC ION
2
1
MAGNESIUM IONMAGNESIUM ION
3
12
1,2-ETHANEDIOL1,2-ETHANEDIOL
4
1
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
1
(4~{a}~{S},8~{a}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one(4~{a}~{S},8~{a}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303