MolNFT v1 · #123984 · protein

PDE4 crystal structure in complex with small molecule inhibitor

5K1I · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “PDE4 crystal structure in complex with small molecule inhibitor”. X-ray diffraction, 3 ligands (6PT, ZN, MG), 20 pockets (best druggability 0.77). MolNFT v1 #123984 on GenesisL1: 3D…

PDB: 5K1I
Type: protein
Length: 2,590 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-specific 3',5'-cyclic phosphodiesterase 4D
EC: 3.1.4.53
UniProt: Q08499
Ligands: 6PT, ZN, MG
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	322	66% helix, 1% strand	Q08499
B, D, F, H	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	326	68% helix, 1% strand	Q08499
C, E	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	321	69% helix, 0% strand	Q08499

Ligands and binding sites

6PT · 4-[(5-acetyl-2-ethyl-3-oxo-6-phenyl-2,3-dihydropyridazin-4-yl)amino]benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.77	0.79	81	empty
2	1021	0.76	0.78	83	empty
3	425	0.71	0.81	41	6PT, MG
4	452	0.70	0.81	44	6PT, MG
5	599	0.70	0.79	53	empty

Interfaces

10 interfaces between chains.

C–D · 787 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 781 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 774 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 758 Å² buried · 14 hydrogen bonds · protein-protein
B–G · 487 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5K1I · PDE4 crystal structure in complex with small molecule inhibitor · the same entry in another collection · chain H against H, 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 5K1I · PDBe 5K1I · UniProt Q08499

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