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

Protein crystallography data

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

Other elements in 8cj7:

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

Zinc (Zn) 3 atoms
Iodine (I) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 6 binding sites of Potassium where determined in the HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor, PDB code: 8cj7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K 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:K801

b:9.6
occ:1.00
 O A:ASP612 2.6 7.8 1.0
O A:LEU634 2.7 8.9 1.0
OG A:SER633 2.7 10.9 1.0
O A:HIS614 2.7 5.8 1.0
O A:ASP610 2.8 8.2 1.0
OD1 A:ASP610 2.9 8.0 1.0
CG A:ASP610 3.3 8.2 1.0
C A:ASP610 3.5 8.6 1.0
C A:LEU634 3.7 9.7 1.0
C A:HIS614 3.7 9.6 1.0
C A:ASP612 3.7 7.9 1.0
CB A:ASP610 3.8 7.0 1.0
N A:LEU634 3.9 6.1 1.0
N A:ASP612 3.9 4.7 1.0
CB A:SER633 3.9 7.2 1.0
CB A:HIS635 3.9 6.1 1.0
OD2 A:ASP610 4.0 10.6 1.0
N A:TRP611 4.2 5.8 1.0
C A:TRP611 4.2 8.4 1.0
CA A:HIS615 4.3 7.0 1.0
ND1 A:HIS635 4.3 10.6 1.0
CA A:ASP612 4.3 5.9 1.0
CA A:ASP610 4.3 6.3 1.0
CA A:SER633 4.3 5.7 1.0
N A:HIS615 4.4 6.4 1.0
CB A:ASP612 4.4 5.1 1.0
CA A:TRP611 4.4 7.2 1.0
N A:HIS614 4.4 8.0 1.0
C A:SER633 4.4 9.9 1.0
N A:GLY616 4.4 7.8 1.0
CA A:HIS635 4.5 7.3 1.0
O A:HOH931 4.5 6.5 1.0
N A:HIS635 4.5 8.6 1.0
CA A:LEU634 4.5 5.6 1.0
CG A:HIS635 4.6 8.7 1.0
OH A:TYR631 4.7 10.1 1.0
C A:VAL613 4.7 10.6 1.0
C A:HIS615 4.7 9.7 1.0
CA A:HIS614 4.7 7.5 1.0
CE1 A:HIS573 4.7 7.5 1.0
N A:VAL613 4.8 6.1 1.0
ND1 A:HIS573 4.8 9.8 1.0
O A:TRP611 4.9 8.9 1.0

Potassium binding site 2 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K 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:K802

b:13.9
occ:1.00
 O A:PHE623 2.6 12.7 1.0
O A:VAL629 2.6 11.0 1.0
O A:HOH912 2.7 12.3 1.0
O A:ASP626 2.8 15.8 1.0
O A:TYR662 2.9 11.0 1.0
O A:HOH1049 3.0 10.0 1.0
C A:PHE623 3.5 13.3 1.0
CB A:PHE623 3.6 10.0 1.0
C A:TYR662 3.7 12.9 1.0
CB A:TYR662 3.7 12.5 1.0
C A:VAL629 3.8 11.1 1.0
C A:ASP626 4.0 17.0 1.0
CA A:PHE623 4.2 8.3 1.0
CA A:TYR662 4.3 11.7 1.0
N A:TYR631 4.3 6.5 1.0
N A:GLU624 4.4 11.0 1.0
N A:ASP626 4.5 14.9 1.0
CB A:ASP626 4.5 17.7 1.0
N A:ASN663 4.5 10.3 1.0
CA A:ASP626 4.5 15.3 1.0
CA A:LEU630 4.6 7.0 1.0
CA A:GLU624 4.6 11.2 1.0
N A:LEU630 4.6 7.3 1.0
CB A:TYR631 4.7 7.1 1.0
C A:GLU624 4.8 14.2 1.0
O A:GLU624 4.8 13.6 1.0
CA A:ASN663 4.9 9.6 1.0
CA A:VAL629 4.9 9.2 1.0
C A:LEU630 4.9 11.6 1.0
CB A:ASN663 4.9 12.4 1.0
O A:GLY659 4.9 23.9 1.0
CG A:PHE623 4.9 10.6 1.0
CG A:TYR662 5.0 14.4 1.0

Potassium binding site 3 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K binding site number 3 of HDAC6 Selective Degraded (Difluoromethyl)-1,3,4-Oxadiazole Substrate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K801

b:12.8
occ:1.00
 O B:ASP612 2.5 11.9 1.0
O B:LEU634 2.7 11.1 1.0
O B:HIS614 2.7 11.8 1.0
OG B:SER633 2.8 14.4 1.0
O B:ASP610 2.8 8.7 1.0
OD1 B:ASP610 2.8 9.5 1.0
CG B:ASP610 3.3 10.6 1.0
C B:ASP610 3.5 11.1 1.0
C B:ASP612 3.6 11.6 1.0
C B:LEU634 3.7 12.8 1.0
C B:HIS614 3.7 13.3 1.0
N B:ASP612 3.7 7.9 1.0
CB B:ASP610 3.8 10.2 1.0
N B:LEU634 3.9 11.1 1.0
CB B:HIS635 4.0 10.5 1.0
CB B:SER633 4.0 8.4 1.0
OD2 B:ASP610 4.0 12.1 1.0
CA B:ASP612 4.1 7.1 1.0
N B:TRP611 4.2 9.5 1.0
C B:TRP611 4.2 13.2 1.0
CB B:ASP612 4.2 6.9 1.0
CA B:ASP610 4.3 8.8 1.0
CA B:HIS615 4.3 10.9 1.0
ND1 B:HIS635 4.3 15.9 1.0
CA B:SER633 4.3 8.3 1.0
CA B:TRP611 4.3 11.0 1.0
N B:HIS615 4.4 10.8 1.0
N B:HIS614 4.4 11.6 1.0
O B:HOH923 4.4 10.4 1.0
CA B:HIS635 4.5 8.8 1.0
C B:SER633 4.5 11.7 1.0
N B:HIS635 4.5 10.6 1.0
N B:GLY616 4.5 8.0 1.0
CA B:LEU634 4.5 10.9 1.0
CG B:HIS635 4.6 14.0 1.0
C B:VAL613 4.7 13.1 1.0
N B:VAL613 4.7 9.2 1.0
CE1 B:HIS573 4.7 12.6 1.0
CA B:HIS614 4.7 10.7 1.0
C B:HIS615 4.8 12.3 1.0
OH B:TYR631 4.8 10.3 1.0
ND1 B:HIS573 4.8 13.6 1.0
O B:TRP611 4.9 10.7 1.0

Potassium binding site 4 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K 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
B:K802

b:16.2
occ:1.00
 O B:PHE623 2.6 14.6 1.0
O B:VAL629 2.6 14.8 1.0
O B:HOH904 2.8 15.8 1.0
O B:ASP626 2.8 18.7 1.0
O B:TYR662 2.9 15.3 1.0
O B:HOH1051 3.0 11.8 1.0
C B:PHE623 3.5 15.3 1.0
C B:TYR662 3.6 16.3 1.0
CB B:TYR662 3.6 14.6 1.0
CB B:PHE623 3.7 11.0 1.0
C B:VAL629 3.8 15.3 1.0
C B:ASP626 4.0 20.5 1.0
CA B:TYR662 4.2 14.0 1.0
CA B:PHE623 4.3 10.1 1.0
N B:TYR631 4.3 12.4 1.0
N B:GLU624 4.4 13.7 1.0
N B:ASN663 4.5 12.7 1.0
N B:ASP626 4.5 19.5 1.0
CA B:ASP626 4.5 19.4 1.0
CB B:ASP626 4.5 21.9 1.0
CA B:LEU630 4.6 10.7 1.0
CA B:GLU624 4.6 13.9 1.0
N B:LEU630 4.6 11.3 1.0
CB B:TYR631 4.7 12.3 1.0
C B:GLU624 4.7 17.5 1.0
O B:GLU624 4.7 17.8 1.0
CA B:ASN663 4.8 12.3 1.0
CB B:ASN663 4.8 15.4 1.0
O B:GLY659 4.9 21.3 1.0
CA B:VAL629 4.9 11.8 1.0
C B:LEU630 4.9 15.3 1.0
CG B:TYR662 4.9 16.2 1.0
CG B:PHE623 5.0 12.3 1.0

Potassium binding site 5 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K 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
C:K801

b:31.9
occ:1.00
 O C:ASP612 2.5 30.7 1.0
O C:LEU634 2.7 34.5 1.0
O C:HIS614 2.7 33.2 1.0
OG C:SER633 2.8 37.5 1.0
OD1 C:ASP610 2.8 31.6 1.0
O C:ASP610 2.9 30.7 1.0
CG C:ASP610 3.3 34.5 1.0
C C:ASP610 3.5 32.2 1.0
C C:ASP612 3.6 30.5 1.0
C C:HIS614 3.7 34.4 1.0
C C:LEU634 3.7 36.5 1.0
CB C:ASP610 3.8 30.6 1.0
N C:ASP612 3.8 25.9 1.0
N C:LEU634 3.9 36.4 1.0
CB C:HIS635 3.9 35.2 1.0
CB C:SER633 4.0 38.0 1.0
OD2 C:ASP610 4.0 34.1 1.0
CA C:ASP612 4.2 26.6 1.0
C C:TRP611 4.2 29.1 1.0
N C:TRP611 4.2 27.8 1.0
CA C:HIS615 4.3 34.9 1.0
ND1 C:HIS635 4.3 40.5 1.0
CA C:ASP610 4.3 28.5 1.0
CB C:ASP612 4.3 28.0 1.0
CA C:SER633 4.3 35.8 1.0
N C:HIS614 4.4 29.8 1.0
N C:HIS615 4.4 33.7 1.0
CA C:TRP611 4.4 27.3 1.0
O C:HOH919 4.4 21.1 1.0
CA C:HIS635 4.4 34.3 1.0
N C:HIS635 4.5 34.6 1.0
C C:SER633 4.5 40.4 1.0
CA C:LEU634 4.5 35.2 1.0
N C:GLY616 4.6 35.9 1.0
CG C:HIS635 4.6 38.5 1.0
C C:VAL613 4.6 32.8 1.0
CA C:HIS614 4.7 30.4 1.0
N C:VAL613 4.7 27.0 1.0
OH C:TYR631 4.8 39.1 1.0
CE1 C:HIS573 4.8 32.8 1.0
C C:HIS615 4.8 38.0 1.0
ND1 C:HIS573 4.8 33.4 1.0
O C:TRP611 4.9 28.1 1.0

Potassium binding site 6 out of 6 in 8cj7

Go back to Potassium Binding Sites List in 8cj7
Potassium 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 Potassium with other atoms in the K 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:K802

b:53.1
occ:1.00
 O C:VAL629 2.6 45.4 1.0
O C:PHE623 2.6 54.4 1.0
O C:ASP626 2.8 57.7 1.0
O C:HOH909 2.9 32.9 1.0
O C:TYR662 2.9 49.8 1.0
CB C:TYR662 3.6 52.9 1.0
C C:PHE623 3.6 53.3 1.0
C C:TYR662 3.6 53.6 1.0
CB C:PHE623 3.7 46.1 1.0
C C:VAL629 3.8 46.6 1.0
C C:ASP626 3.9 57.5 1.0
CA C:TYR662 4.2 51.4 1.0
CA C:PHE623 4.3 46.3 1.0
N C:TYR631 4.4 40.6 1.0
N C:ASP626 4.5 54.9 1.0
N C:ASN663 4.5 51.6 1.0
CB C:ASP626 4.5 54.4 1.0
CA C:ASP626 4.5 53.7 1.0
N C:GLU624 4.5 51.1 1.0
CA C:LEU630 4.6 43.2 1.0
N C:LEU630 4.7 43.7 1.0
CB C:TYR631 4.7 39.8 1.0
CA C:GLU624 4.7 52.3 1.0
O C:GLU624 4.8 57.9 1.0
O C:GLY659 4.8 65.2 1.0
C C:GLU624 4.8 58.3 1.0
CA C:VAL629 4.8 42.3 1.0
CG C:TYR662 4.9 54.5 1.0
CA C:ASN663 4.9 50.8 1.0
CB C:ASN663 4.9 52.0 1.0
C C:LEU630 4.9 44.6 1.0
CG C:PHE623 5.0 45.3 1.0

Reference:

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
Page generated: Mon Aug 12 22:55:55 2024

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