MolNFT v1 · #144877 · protein

Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)- 1-(2-chlorophenyl)-4-methyl-[1,2,4]TRIAZOLO[4,3-A]QUINOXALINE-8- carboxamide

6C7D · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “Crystal structure of human phosphodiesterase 2A with N-(1-adamantyl)…”. X-ray diffraction, 3 ligands (EOJ, ZN, MG), 15 pockets (best druggability 0.83). MolNFT v1 #144877 on GenesisL1…

PDB: 6C7D
Type: protein
Length: 1,336 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: EOJ, ZN, MG
Pockets: 15 · best druggability 0.83

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	342	70% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	339	69% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	327	69% helix, 0% strand	O00408
D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	328	69% helix, 0% strand	O00408

Ligands and binding sites

EOJ · 1-(2-chlorophenyl)-4-methyl-N-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl][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

15 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	736	0.83	0.86	61	EOJ, MG
2	977	0.75	0.78	87	empty
3	397	0.74	0.85	40	EOJ, MG
4	378	0.73	0.84	38	EOJ, MG
5	356	0.72	0.84	38	EOJ, MG

Interfaces

5 interfaces between chains.

C–D · 913 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 805 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 751 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 470 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 109 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6C7D · Crystal structure of human phosphodiesterase 2A 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 6C7D · PDBe 6C7D · UniProt O00408

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