MolNFT v1 · #149216 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-048

6FTW · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-048”. X-ray diffraction, 3 ligands (E6Z, ZN, MG), 13 pockets (best druggability 0.77). MolNFT v1…

PDB: 6FTW
Type: protein
Length: 1,304 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: E6Z, ZN, MG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 4 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	331	68% helix, 0% strand	Q08499
B	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499
C	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	68% helix, 1% strand	Q08499
D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	325	66% helix, 1% strand	Q08499

Ligands and binding sites

E6Z · 3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide · 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
EDO · 1,2-ethanediol · additive · 39 copies · chains A, C, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.77	0.92	34	EDO
2	445	0.72	0.82	40	MG, EDO, E6Z
3	407	0.72	0.83	39	MG, EDO, E6Z
4	448	0.72	0.82	43	MG, EDO, E6Z
5	142	0.71	0.91	26	EDO

Interfaces

6 interfaces between chains.

A–C · 926 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 919 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 820 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 762 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 252 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6FTW · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048 · 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 6FTW · PDBe 6FTW · UniProt Q08499

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.