MolNFT v1 · #14775 · protein

Crystal structure of PDE4D catalytic domain and zardaverine complex

1MKD · Phosphodiesterase 4D: “Crystal structure of PDE4D catalytic domain and zardaverine complex”. X-ray diffraction, 3 ligands (ZAR, ZN, MG), 20 pockets (best druggability 0.80). MolNFT v1 #14775 on GenesisL1: 3D structure, binding sites…

PDB: 1MKD
Type: protein
Length: 3,936 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphodiesterase 4D
EC: 3.1.4.17
UniProt: Q08499
Ligands: ZAR, ZN, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Phosphodiesterase 4D (EC 3.1.4.17)	protein	328	66% helix, 1% strand	Q08499

Ligands and binding sites

ZAR · 6-(4-difluoromethoxy-3-methoxy-phenyl)-2H-pyridazin-3-one · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	889	0.80	0.82	76	MG, ZAR
2	618	0.78	0.84	61	ZN, MG, ZAR
3	589	0.77	0.83	58	MG, ZAR
4	764	0.77	0.81	71	MG, ZAR
5	600	0.77	0.83	66	MG, ZAR

Interfaces

24 interfaces between chains.

F–G · 794 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 782 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 781 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 767 Å² buried · 11 hydrogen bonds · protein-protein
E–H · 766 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1MKD · crystal structure of PDE4D catalytic domain and zardaverine complex · the same entry in another collection · chain F against F, 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 1MKD · PDBe 1MKD · UniProt Q08499

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