MolNFT v1 · #149197 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-3098

6FTA: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-3098”. X-ray diffraction, 3 ligands (E6N, ZN, MG). MolNFT v1 #149197 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FTA
Type: protein
Length: 1,300 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q08499
Ligands: E6N, ZN, MG

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	329	—	Q08499
B	—	protein	324	—	Q08499
C	—	protein	323	—	Q08499
D	—	protein	324	—	Q08499

Ligands and binding sites

E6N · (4~{A}~{S},8~{A}~{S})-4-[4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl]-2-[1-(3-nitroimidazo[1, 2-b]pyridazin-6-yl)piperidin-4-yl]-4~{A},5,6,7,8, 8~{A}-hexahydrophthalazin-1-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 · 29 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D

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

Compared structures

6FTA · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098 · 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 6FTA · PDBe 6FTA · UniProt Q08499

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