MolNFT v1 · #172720 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-769

7ABE: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-769”. X-ray diffraction, 3 ligands (J2E, ZN, MG). MolNFT v1 #172720 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ABE
Type: protein
Length: 1,304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q08499
Ligands: J2E, ZN, MG

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	330	—	Q08499
B	—	protein	324	—	Q08499
C	—	protein	326	—	Q08499
D	—	protein	324	—	Q08499

Ligands and binding sites

J2E · 1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4, 4-dimethyl-4,5-dihydro-1H-pyrazol-5-one · 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 · 50 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D

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

Compared structures

7ABE · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-769 · the same entry in another collection · chain D against D, 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 7ABE · PDBe 7ABE · UniProt Q08499

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