Zinc in PDB 8f1c: Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4)

The structure of Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) (pdb code 8f1c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4), PDB code: 8f1c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:89.9 occ:1.00 HB3 D:CYS83 1.9 46.3 1.0 CB D:CYS83 2.2 44.8 1.0 HB2 D:CYS83 2.2 46.6 1.0 ND1 A:HIS77 2.3 41.9 1.0 SG A:CYS104 2.3 53.9 1.0 SG D:CYS83 2.3 61.8 1.0 HE1 A:HIS77 2.9 39.2 1.0 CE1 A:HIS77 2.9 40.1 1.0 HB3 A:CYS105 3.4 46.4 1.0 HD2 D:PRO85 3.4 42.1 1.0 HB2 A:CYS104 3.4 44.4 1.0 CG A:HIS77 3.5 39.0 1.0 HB3 A:HIS77 3.5 38.9 1.0 CB A:CYS104 3.6 45.7 1.0 SG A:CYS105 3.6 50.5 1.0 CA D:CYS83 3.7 44.7 1.0 HG2 D:PRO85 3.9 42.5 1.0 CB A:CYS105 4.0 49.9 1.0 CB A:HIS77 4.0 40.3 1.0 HA D:CYS83 4.1 45.5 1.0 NE2 A:HIS77 4.1 39.4 1.0 HB3 A:CYS104 4.2 44.3 1.0 CD D:PRO85 4.3 39.0 1.0 HB2 D:PRO85 4.3 42.4 1.0 H D:CYS83 4.3 45.6 1.0 CD2 A:HIS77 4.4 36.1 1.0 C A:CYS104 4.4 43.4 1.0 N A:CYS105 4.4 43.4 1.0 HB2 A:GLU102 4.4 44.2 1.0 C D:CYS83 4.5 49.1 1.0 H A:CYS105 4.5 45.3 1.0 CG D:PRO85 4.5 43.5 1.0 H D:LEU86 4.5 38.9 1.0 N D:CYS83 4.6 46.6 1.0 CA A:CYS104 4.6 48.7 1.0 HA A:HIS77 4.7 39.4 1.0 HB2 A:HIS77 4.7 39.6 1.0 HB2 A:CYS105 4.7 46.5 1.0 HG A:CYS105 4.7 45.8 1.0 O A:CYS104 4.8 41.4 1.0 H D:GLY84 4.8 40.9 1.0 CA A:CYS105 4.8 47.9 1.0 HD3 D:PRO85 4.8 41.8 1.0 N D:GLY84 4.9 43.0 1.0 CB D:PRO85 4.9 40.8 1.0 H A:CYS104 5.0 44.0 1.0

Zinc binding site 2 out of 4 in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:89.9 occ:1.00 HB3 A:CYS83 1.9 46.3 1.0 CB A:CYS83 2.2 44.8 1.0 HB2 A:CYS83 2.2 46.6 1.0 SG A:CYS83 2.3 61.8 1.0 ND1 B:HIS77 2.3 41.9 1.0 SG B:CYS104 2.3 53.9 1.0 HE1 B:HIS77 2.9 39.2 1.0 CE1 B:HIS77 2.9 40.1 1.0 HB3 B:CYS105 3.4 46.4 1.0 HD2 A:PRO85 3.4 42.1 1.0 HB2 B:CYS104 3.4 44.4 1.0 CG B:HIS77 3.5 39.0 1.0 HB3 B:HIS77 3.5 38.9 1.0 CB B:CYS104 3.6 45.7 1.0 SG B:CYS105 3.6 50.5 1.0 CA A:CYS83 3.7 44.7 1.0 HG2 A:PRO85 3.9 42.5 1.0 CB B:CYS105 4.0 49.9 1.0 CB B:HIS77 4.0 40.3 1.0 HA A:CYS83 4.0 45.5 1.0 NE2 B:HIS77 4.1 39.4 1.0 HB3 B:CYS104 4.2 44.3 1.0 CD A:PRO85 4.3 39.0 1.0 HB2 A:PRO85 4.3 42.4 1.0 H A:CYS83 4.3 45.6 1.0 CD2 B:HIS77 4.4 36.1 1.0 C B:CYS104 4.4 43.4 1.0 N B:CYS105 4.4 43.4 1.0 HB2 B:GLU102 4.4 44.2 1.0 C A:CYS83 4.5 49.1 1.0 H B:CYS105 4.5 45.3 1.0 CG A:PRO85 4.5 43.5 1.0 H A:LEU86 4.5 38.9 1.0 N A:CYS83 4.5 46.6 1.0 CA B:CYS104 4.6 48.7 1.0 HA B:HIS77 4.7 39.4 1.0 HB2 B:HIS77 4.7 39.6 1.0 HB2 B:CYS105 4.7 46.5 1.0 HG B:CYS105 4.7 45.8 1.0 O B:CYS104 4.8 41.4 1.0 H A:GLY84 4.8 40.9 1.0 CA B:CYS105 4.8 47.9 1.0 HD3 A:PRO85 4.8 41.8 1.0 N A:GLY84 4.9 43.0 1.0 CB A:PRO85 4.9 40.8 1.0 H B:CYS104 5.0 44.0 1.0

Zinc binding site 3 out of 4 in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:89.9 occ:1.00 HB3 B:CYS83 1.9 46.3 1.0 CB B:CYS83 2.2 44.8 1.0 HB2 B:CYS83 2.2 46.6 1.0 SG B:CYS83 2.3 61.8 1.0 ND1 C:HIS77 2.3 41.9 1.0 SG C:CYS104 2.3 53.9 1.0 HE1 C:HIS77 2.9 39.2 1.0 CE1 C:HIS77 2.9 40.1 1.0 HB3 C:CYS105 3.4 46.4 1.0 HD2 B:PRO85 3.4 42.1 1.0 HB2 C:CYS104 3.4 44.4 1.0 CG C:HIS77 3.5 39.0 1.0 HB3 C:HIS77 3.5 38.9 1.0 CB C:CYS104 3.6 45.7 1.0 SG C:CYS105 3.6 50.5 1.0 CA B:CYS83 3.7 44.7 1.0 HG2 B:PRO85 3.9 42.5 1.0 CB C:CYS105 4.0 49.9 1.0 CB C:HIS77 4.0 40.3 1.0 HA B:CYS83 4.0 45.5 1.0 NE2 C:HIS77 4.1 39.4 1.0 HB3 C:CYS104 4.2 44.3 1.0 CD B:PRO85 4.3 39.0 1.0 HB2 B:PRO85 4.3 42.4 1.0 H B:CYS83 4.3 45.6 1.0 CD2 C:HIS77 4.4 36.1 1.0 C C:CYS104 4.4 43.4 1.0 N C:CYS105 4.4 43.4 1.0 HB2 C:GLU102 4.4 44.2 1.0 C B:CYS83 4.5 49.1 1.0 H C:CYS105 4.5 45.3 1.0 CG B:PRO85 4.5 43.5 1.0 H B:LEU86 4.5 38.9 1.0 N B:CYS83 4.5 46.6 1.0 CA C:CYS104 4.6 48.7 1.0 HA C:HIS77 4.7 39.4 1.0 HB2 C:HIS77 4.7 39.6 1.0 HB2 C:CYS105 4.7 46.5 1.0 HG C:CYS105 4.7 45.8 1.0 H B:GLY84 4.8 40.9 1.0 O C:CYS104 4.8 41.4 1.0 HD3 B:PRO85 4.8 41.8 1.0 CA C:CYS105 4.8 47.9 1.0 N B:GLY84 4.9 43.0 1.0 CB B:PRO85 4.9 40.8 1.0 H C:CYS104 5.0 44.0 1.0

Zinc binding site 4 out of 4 in the Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Voltage-Gated Potassium Channel KV3.1 with Novel Positive Modulator (9M)-9-{5-Chloro-6-[(3,3-Dimethyl-2,3-Dihydro-1-Benzofuran-4-Yl)Oxy]- 4-Methylpyridin-3-Yl}-2-Methyl-7,9-Dihydro-8H-Purin-8-One (Compound 4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:89.9 occ:1.00 HB3 C:CYS83 1.9 46.3 1.0 CB C:CYS83 2.2 44.8 1.0 HB2 C:CYS83 2.2 46.6 1.0 ND1 D:HIS77 2.3 41.9 1.0 SG D:CYS104 2.3 53.9 1.0 SG C:CYS83 2.3 61.8 1.0 HE1 D:HIS77 2.9 39.2 1.0 CE1 D:HIS77 2.9 40.1 1.0 HB3 D:CYS105 3.4 46.4 1.0 HD2 C:PRO85 3.4 42.1 1.0 HB2 D:CYS104 3.4 44.4 1.0 CG D:HIS77 3.5 39.0 1.0 HB3 D:HIS77 3.5 38.9 1.0 CB D:CYS104 3.6 45.7 1.0 SG D:CYS105 3.6 50.5 1.0 CA C:CYS83 3.7 44.7 1.0 HG2 C:PRO85 3.9 42.5 1.0 CB D:CYS105 4.0 49.9 1.0 CB D:HIS77 4.0 40.3 1.0 HA C:CYS83 4.0 45.5 1.0 NE2 D:HIS77 4.1 39.4 1.0 HB3 D:CYS104 4.2 44.3 1.0 CD C:PRO85 4.3 39.0 1.0 HB2 C:PRO85 4.3 42.4 1.0 H C:CYS83 4.3 45.6 1.0 CD2 D:HIS77 4.4 36.1 1.0 C D:CYS104 4.4 43.4 1.0 N D:CYS105 4.4 43.4 1.0 HB2 D:GLU102 4.4 44.2 1.0 C C:CYS83 4.5 49.1 1.0 CG C:PRO85 4.5 43.5 1.0 H D:CYS105 4.5 45.3 1.0 H C:LEU86 4.5 38.9 1.0 N C:CYS83 4.6 46.6 1.0 CA D:CYS104 4.6 48.7 1.0 HA D:HIS77 4.7 39.4 1.0 HB2 D:HIS77 4.7 39.6 1.0 HB2 D:CYS105 4.7 46.5 1.0 HG D:CYS105 4.7 45.8 1.0 H C:GLY84 4.8 40.9 1.0 O D:CYS104 4.8 41.4 1.0 HD3 C:PRO85 4.8 41.8 1.0 CA D:CYS105 4.8 47.9 1.0 N C:GLY84 4.9 43.0 1.0 CB C:PRO85 4.9 40.8 1.0 H D:CYS104 5.0 44.0 1.0

Y.T.Chen, M.R.Hong, X.J.Zhang, J.Kostas, Y.Li, R.L.Kraus, V.P.Santarelli, D.Wang, Y.Gomez-Llorente, A.Brooun, C.Strickland, S.M.Soisson, D.J.Klein, A.T.Ginnetti, M.J.Marino, S.J.Stachel, A.Ishchenko. Identification and Structural and Biophysical Characterization of A Positive Modulator of Human KV3.1 Channels. Proc.Natl.Acad.Sci.Usa V. 120 29120 2023.
ISSN: ESSN 1091-6490
PubMed: 37812700
DOI: 10.1073/PNAS.2220029120