MolNFT v1 · #148714 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1439

6FET · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1439”. X-ray diffraction, 4 ligands (D68, ZN, MG), 14 pockets (best druggability 0.83). MolNFT v1…

PDB: 6FET
Type: protein
Length: 1,300 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-specific 3',5'-cyclic phosphodiesterase 4D
EC: 3.1.4.53
UniProt: Q08499
Ligands: D68, ZN, MG, NI
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	329	67% helix, 1% strand	Q08499
B	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	323	67% helix, 1% strand	Q08499
C, D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499

Ligands and binding sites

D68 · 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
NI · Nickel (II) ion · metal · 2 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 67 copies · chains A, C, D, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.83	0.89	71	EDO
2	990	0.79	0.81	94	EDO, PEG
3	247	0.77	0.90	40	EDO, PEG
4	246	0.77	0.90	37	EDO
5	463	0.72	0.82	47	MG, EDO, D68

Interfaces

6 interfaces between chains.

A–C · 990 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 946 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 675 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 641 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 238 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6FET · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q08499
Elsewhere: RCSB PDB 6FET · PDBe 6FET · UniProt Q08499

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