Research workbench

Crystal structure of human phosphodiesterase 2A in complex with 6- methyl-N-(1-(4-(TRIFLUOROMETHOXY)PHENYL)PROPYL)PYRAZOLO[1,5- A]PYRIMIDINE-3-carboxamide

Analyse Crystal structure of human phosphodiesterase 2A in complex with 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XKM
Type: protein
Length: 2,005 residues
Chains: 6
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: 87R, MG, ZN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 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	70% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	345	70% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	343	69% helix, 0% strand	O00408
D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	337	68% helix, 0% strand	O00408
E	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	319	69% helix, 0% strand	O00408
F	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	321	68% helix, 0% strand	O00408

Ligands and binding sites

87R · 6-methyl-N-[(1R)-1-[4-(trifluoromethyloxy) phenyl]propyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1080	0.84	0.85	102	MG, 87R
2	441	0.78	0.86	40	MG, 87R
3	400	0.77	0.86	41	MG, 87R
4	429	0.77	0.86	41	MG, 87R
5	425	0.77	0.86	43	MG, 87R

Interfaces

10 interfaces between chains.

A–E · 1482 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1448 Å² buried · 20 hydrogen bonds · protein-protein
D–F · 1425 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 497 Å² buried · 1 hydrogen bond · protein-protein
D–E · 380 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5XKM · Crystal structure of human phosphodiesterase 2A in complex with… · 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 5XKM · PDBe 5XKM · UniProt O00408

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