MolNFT v1 · #88614 · protein

PDE2A catalytic domain in complex with a brain penetrant inhibitor

4D09 · Cgmp-dependent 3', 5'-cyclic phosphodiesterase: “PDE2A catalytic domain in complex with a brain penetrant inhibitor”. X-ray diffraction, 3 ligands (788, ZN, MG), 14 pockets (best druggability 0.73). MolNFT v1 #88614 on GenesisL1: 3D…

PDB: 4D09
Type: protein
Length: 1,333 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-dependent 3', 5'-cyclic phosphodiesterase
EC: 3.1.4.17
UniProt: O00408
Ligands: 788, ZN, MG
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	340	69% helix, 0% strand	O00408
B	Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	338	69% helix, 0% strand	O00408
C	Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	329	70% helix, 0% strand	O00408
D	Cgmp-dependent 3', 5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	326	69% helix, 0% strand	O00408

Ligands and binding sites

788 · N-benzyl-4-methyl-1-phenyl[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · 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

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.73	0.85	36	788, MG
2	338	0.73	0.85	41	788, MG
3	583	0.72	0.80	67	empty
4	365	0.71	0.83	36	788, MG
5	325	0.71	0.84	38	788, MG

Interfaces

6 interfaces between chains.

A–B · 728 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 386 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 343 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 197 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 104 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4D09 · PDE2a catalytic domain in complex with a brain penetrant inhibitor · 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 O00408
Elsewhere: RCSB PDB 4D09 · PDBe 4D09 · UniProt O00408

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