Iodine in PDB 8cj7: HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor

The structure of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor, PDB code: 8cj7 was solved by J.Sandmark, M.Ek, L.Ripa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.19 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.977, 84.062, 96.132, 90, 110.25, 90
R / Rfree (%)	20.6 / 22.7

The structure of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor also contains other interesting chemical elements:

Zinc	(Zn)	3 atoms
Potassium	(K)	6 atoms

The binding sites of Iodine atom in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor (pdb code 8cj7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor, PDB code: 8cj7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I805 b:24.5 occ:1.00 O A:HOH1155 3.6 58.0 1.0 NE2 A:HIS463 3.6 14.3 1.0 C A:SER531 3.8 12.3 1.0 N A:ILE532 3.8 9.8 1.0 CD2 A:HIS463 4.0 14.7 1.0 CA A:SER531 4.0 10.3 1.0 C A:ILE532 4.1 11.8 1.0 O A:ILE532 4.2 11.5 1.0 O A:SER531 4.3 8.0 1.0 CE1 A:PHE583 4.3 11.3 1.0 CA A:ILE532 4.4 7.7 1.0 N A:PHE533 4.4 7.3 1.0 CB A:SER531 4.5 11.4 1.0 N11 A:UTO804 4.5 41.6 1.0 CD2 A:PHE533 4.5 13.6 1.0 C12 A:UTO804 4.6 42.4 1.0 CD1 A:PHE583 4.7 10.3 1.0 CE1 A:HIS463 4.8 13.1 1.0 CB A:PHE533 4.8 9.8 1.0 O A:HOH984 5.0 8.6 1.0 O A:HOH951 5.0 34.1 1.0

Iodine binding site 2 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I806 b:15.4 occ:1.00 NE1 A:TRP459 3.6 18.5 1.0 CA A:ARG520 4.0 15.9 1.0 N A:ARG520 4.2 15.8 1.0 CD1 A:TRP459 4.4 19.0 1.0 CB A:ASN523 4.4 15.0 1.0 C A:PRO519 4.4 17.6 1.0 O A:PRO519 4.4 15.1 1.0 CB A:ARG520 4.4 19.6 1.0 CE2 A:TRP459 4.6 18.8 1.0 CG A:ASN523 4.7 21.3 1.0 ND2 A:ASN523 4.7 23.5 1.0 CB A:PRO519 4.8 19.0 1.0 CZ2 A:TRP459 5.0 17.3 1.0

Iodine binding site 3 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range:

Iodine binding site 4 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I808 b:47.0 occ:1.00 O A:HOH1073 3.4 41.1 1.0 N A:SER484 3.4 18.7 1.0 CB A:SER484 3.7 19.6 1.0 OG A:SER484 3.7 31.3 1.0 CA A:ARG481 3.7 19.8 1.0 O A:GLU478 3.9 20.1 1.0 CB A:LEU483 3.9 17.3 1.0 C A:ARG481 4.0 23.4 1.0 N A:LEU483 4.1 16.6 1.0 CA A:GLU478 4.2 16.9 1.0 CA A:SER484 4.2 17.8 1.0 CA A:LEU483 4.3 16.8 1.0 C A:LEU483 4.3 21.0 1.0 O A:ARG481 4.4 23.7 1.0 N A:LEU482 4.4 18.0 1.0 CB A:ARG481 4.5 21.9 1.0 C A:GLU478 4.5 21.9 1.0 O A:HIS477 4.6 17.9 1.0 N A:ARG481 4.6 19.0 1.0 CD A:ARG481 4.7 45.6 1.0 CB A:GLU478 4.8 18.2 1.0 CG A:LEU483 4.8 21.4 1.0 C A:LEU482 4.9 20.6 1.0 CD2 A:LEU483 5.0 23.7 1.0

Iodine binding site 5 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:I805 b:71.5 occ:1.00 N B:SER484 3.4 28.7 1.0 OG B:SER484 3.7 42.1 1.0 CB B:SER484 3.7 33.5 1.0 CA B:ARG481 3.7 25.1 1.0 O B:GLU478 3.9 28.0 1.0 CB B:LEU483 3.9 24.9 1.0 C B:ARG481 4.0 28.0 1.0 N B:LEU483 4.1 24.5 1.0 CA B:GLU478 4.1 24.1 1.0 CA B:SER484 4.2 29.1 1.0 CA B:LEU483 4.3 24.8 1.0 C B:LEU483 4.3 30.2 1.0 O B:ARG481 4.4 28.9 1.0 N B:LEU482 4.4 23.3 1.0 C B:GLU478 4.5 29.2 1.0 CB B:ARG481 4.5 26.2 1.0 O B:HIS477 4.6 26.5 1.0 N B:ARG481 4.6 24.8 1.0 CB B:GLU478 4.8 25.6 1.0 CG B:LEU483 4.8 29.1 1.0 O B:HOH1139 4.9 35.7 1.0 C B:LEU482 4.9 26.9 1.0 CD2 B:LEU483 5.0 30.1 1.0 CG B:ARG481 5.0 38.2 1.0

Iodine binding site 6 out of 6 in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:I804 b:46.1 occ:1.00 CD C:PRO711 3.9 34.4 1.0 CG C:PRO711 3.9 38.9 1.0 ND2 C:ASN746 3.9 22.4 1.0 CB C:ASN746 4.1 25.7 1.0 CA C:ASN746 4.1 22.9 1.0 O C:HOH999 4.1 41.0 1.0 CG C:ASN746 4.2 30.7 1.0 O C:GLY709 4.2 29.7 1.0 CB C:PRO711 4.4 34.6 1.0 O C:TYR745 4.6 24.2 1.0 N C:PRO711 4.9 31.9 1.0 N C:ASN746 4.9 22.3 1.0 OD1 C:ASN746 5.0 21.9 1.0

L.Ripa, J.Sandmark, G.Hughes, I.Shamovsky, A.Gunnarsson, J.Johansson, A.Llinas, M.Collins, B.Jung, A.Noven, N.Pemberton, M.Mogemark, Y.Xiong, Q.Li, S.Tangefjord, M.Ek, A.Astrand. Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37797307
DOI: 10.1021/ACS.JMEDCHEM.3C01269