MolNFT v1 · #142949 · protein

Crystal structure of the PDE4D catalytic domain in complex with osthole

6AKR · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain in complex with osthole”. X-ray diffraction, 2 ligands (A0O, ZN), 9 pockets (best druggability 0.73). MolNFT v1 #142949 on GenesisL1…

PDB: 6AKR
Type: protein
Length: 1,303 residues
Chains: 4
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: A0O, ZN
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	325	67% helix, 1% strand	Q08499
B	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	329	67% helix, 0% strand	Q08499
C	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	325	67% helix, 1% strand	Q08499
D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499

Ligands and binding sites

A0O · 7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	464	0.73	0.83	38	ZN, A0O
2	1130	0.73	0.76	81	empty
3	447	0.72	0.82	40	ZN, A0O
4	462	0.72	0.82	40	ZN, A0O
5	443	0.71	0.82	41	ZN, A0O

Interfaces

5 interfaces between chains.

B–D · 891 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 502 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 448 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 270 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 66 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6AKR · Crystal structure of the PDE4D catalytic domain in complex with osthole · 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 6AKR · PDBe 6AKR · UniProt Q08499

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