MolNFT v2 · #174713 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-768

7ABD: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-768”. X-ray diffraction at 2.41, 3 ligands (RLW, ZN, MG). MolNFT v2 #174713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ABD
Type: protein
Length: 1,302 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.41
Source: Homo sapiens
UniProt: Q08499
Ligands: RLW, ZN, MG

Structure

x-ray diffraction · resolution 2.41 · 3 distinct chains.

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

Ligands and binding sites

RLW · 3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,4-dimethyl-1~{H}-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 · 30 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 C, D

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

Compared structures

7ABD · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-768 · 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 7ABD · PDBe 7ABD · UniProt Q08499

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