MolNFT v1 · #144272 · protein

Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with BPN5004

6BOJ · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with BPN5004”. X-ray diffraction, 4 ligands (E31, ZN, MG), 13 pockets (best druggability 0.84). MolNFT v1…

PDB: 6BOJ
Type: protein
Length: 1,343 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, Q07343
Ligands: E31, ZN, MG, CL
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	335	67% helix, 1% strand	Q08499, Q07343
C	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	338	67% helix, 1% strand	Q08499, Q07343

Ligands and binding sites

E31 · 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 6 copies · chains A, C, B, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, D, A, C

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.84	0.93	52	MG, E31
2	331	0.82	0.92	49	MG, E31
3	921	0.81	0.83	91	MPD
4	416	0.81	0.89	58	MG, E31
5	528	0.81	0.87	60	empty

Interfaces

5 interfaces between chains.

C–D · 790 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 773 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 727 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 686 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 178 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6BOJ · Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 · 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
Every structure of UniProt Q07343
Elsewhere: RCSB PDB 6BOJ · PDBe 6BOJ · UniProt Q08499 · UniProt Q07343

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