MolNFT v1 · #149188 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-425

6FT0: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-425”. X-ray diffraction, 3 ligands (E6E, ZN, MG). MolNFT v1 #149188 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FT0
Type: protein
Length: 1,301 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q08499
Ligands: E6E, ZN, MG

Structure

x-ray diffraction · 3 distinct chains.

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

Ligands and binding sites

E6E · 4-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-2-(1-{thieno[3,2-d]pyrimidin-4-yl}piperidin-4-yl)-1,2,4A,5, 8,8A-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 · 42 copies · chains A, C, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains D

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

Compared structures

6FT0 · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-425 · the same entry in another collection · chain C against C, 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 6FT0 · PDBe 6FT0 · UniProt Q08499

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