Cobalt in PDB 6ykc: Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic

All present enzymatic activity of Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic:
4.2.1.1;

The structure of Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic, PDB code: 6ykc was solved by M.Kugler, J.Brynda, K.Pospisilova, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.57 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.958, 41.210, 72.138, 90.00, 103.86, 90.00
R / Rfree (%)	14.7 / 17.9

The structure of Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Cobalt atom in the Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic (pdb code 6ykc). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic, PDB code: 6ykc:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:17.1 occ:0.30 CO1 A:OY8302 0.0 17.1 0.3 C1 A:OY5303 1.3 20.5 0.2 C4 A:OY5303 1.3 20.5 0.2 B9 A:OY5303 1.5 21.1 0.2 B7 A:OY5303 1.6 20.5 0.2 B8 A:OY5303 1.7 20.7 0.2 CO1 A:OY5303 1.8 18.0 0.2 B5 A:OY5303 1.8 21.3 0.2 B1 A:OY5303 1.9 21.6 0.2 B6 A:OY5303 2.0 21.3 0.2 C3 A:OY8302 2.0 17.8 0.3 B2 A:OY5303 2.0 21.5 0.2 B9 A:OY8302 2.0 16.0 0.3 B18 A:OY8302 2.1 17.1 0.3 C1 A:OY8302 2.1 17.2 0.3 B3 A:OY5303 2.1 21.7 0.2 C4 A:OY8302 2.1 17.8 0.3 C2 A:OY8302 2.1 16.9 0.3 B14 A:OY8302 2.1 15.7 0.3 B7 A:OY8302 2.1 17.4 0.3 B10 A:OY8302 2.2 16.0 0.3 B8 A:OY8302 2.2 16.6 0.3 B4 A:OY5303 2.2 22.1 0.2 C5 A:OY5303 2.8 21.9 0.2 C5 A:OY8302 3.0 14.2 0.3 C7 A:OY8302 3.1 18.3 0.3 B1 A:OY8302 3.3 16.9 0.3 B16 A:OY8302 3.3 17.6 0.3 B17 A:OY8302 3.4 17.6 0.3 B15 A:OY8302 3.4 18.2 0.3 B2 A:OY8302 3.4 16.7 0.3 B11 A:OY8302 3.4 17.1 0.3 B13 A:OY8302 3.4 17.3 0.3 B6 A:OY8302 3.4 17.9 0.3 B3 A:OY8302 3.4 17.7 0.3 B5 A:OY8302 3.4 17.7 0.3 B18 A:OY5303 3.4 20.7 0.2 B10 A:OY5303 3.5 20.5 0.2 O A:HOH409 3.5 20.0 0.5 C3 A:OY5303 3.6 20.6 0.2 NE2 A:HIS64 3.6 21.4 0.5 B14 A:OY5303 3.6 20.4 0.2 O A:HOH405 3.7 20.4 0.5 C2 A:OY5303 3.7 20.6 0.2 C6 A:OY5303 3.7 22.8 0.2 B12 A:OY8302 3.9 17.9 0.3 NE2 A:GLN92 3.9 14.7 0.6 B4 A:OY8302 4.0 17.6 0.3 C8 A:OY8302 4.0 17.8 0.3 OE1 A:GLN92 4.2 15.4 0.4 C7 A:OY5303 4.2 19.9 0.2 OG1 A:THR199 4.3 18.0 1.0 C6 A:OY8302 4.4 11.6 0.3 CE1 A:HIS64 4.5 19.0 0.5 O A:HOH609 4.5 17.8 0.5 CD2 A:HIS64 4.5 18.7 0.5 NE2 A:GLN92 4.8 15.4 0.4 OE1 A:GLN67 4.8 29.9 1.0 ND2 A:ASN62 4.8 13.6 0.5 B17 A:OY5303 4.9 20.6 0.2 CD A:GLN92 4.9 13.8 0.4 B16 A:OY5303 4.9 21.8 0.2 B11 A:OY5303 5.0 21.8 0.2

Cobalt binding site 2 out of 2 in the Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Metala-Carborane Di-Ethyl-Sulfonamide (Trans Isomer) in Complex with Ca IX Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:18.0 occ:0.20 CO1 A:OY5303 0.0 18.0 0.2 B9 A:OY8302 0.8 16.0 0.3 B8 A:OY8302 1.4 16.6 0.3 C1 A:OY8302 1.5 17.2 0.3 B2 A:OY8302 1.7 16.7 0.3 B1 A:OY8302 1.7 16.9 0.3 CO1 A:OY8302 1.8 17.1 0.3 C4 A:OY8302 2.0 17.8 0.3 B7 A:OY8302 2.0 17.4 0.3 C3 A:OY5303 2.0 20.6 0.2 B7 A:OY5303 2.1 20.5 0.2 C1 A:OY5303 2.1 20.5 0.2 C4 A:OY5303 2.1 20.5 0.2 B18 A:OY5303 2.1 20.7 0.2 B9 A:OY5303 2.1 21.1 0.2 B8 A:OY5303 2.1 20.7 0.2 C2 A:OY5303 2.1 20.6 0.2 B14 A:OY5303 2.1 20.4 0.2 B10 A:OY5303 2.1 20.5 0.2 B3 A:OY8302 2.3 17.7 0.3 B5 A:OY8302 2.3 17.7 0.3 B4 A:OY8302 2.5 17.6 0.3 B6 A:OY8302 2.5 17.9 0.3 C5 A:OY5303 3.0 21.9 0.2 C7 A:OY5303 3.1 19.9 0.2 C3 A:OY8302 3.3 17.8 0.3 B16 A:OY5303 3.3 21.8 0.2 B17 A:OY5303 3.3 20.6 0.2 B6 A:OY5303 3.3 21.3 0.2 B5 A:OY5303 3.3 21.3 0.2 B1 A:OY5303 3.3 21.6 0.2 B3 A:OY5303 3.4 21.7 0.2 B2 A:OY5303 3.4 21.5 0.2 B15 A:OY5303 3.4 21.3 0.2 B11 A:OY5303 3.4 21.8 0.2 B13 A:OY5303 3.4 21.3 0.2 C2 A:OY8302 3.4 16.9 0.3 C5 A:OY8302 3.5 14.2 0.3 B18 A:OY8302 3.5 17.1 0.3 B14 A:OY8302 3.7 15.7 0.3 C7 A:OY8302 3.7 18.3 0.3 B10 A:OY8302 3.8 16.0 0.3 B12 A:OY5303 3.9 21.0 0.2 B4 A:OY5303 3.9 22.1 0.2 OE1 A:GLN92 4.1 15.4 0.4 NE2 A:GLN92 4.2 14.7 0.6 C8 A:OY5303 4.2 21.6 0.2 C6 A:OY5303 4.4 22.8 0.2 C8 A:OY8302 4.4 17.8 0.3 C6 A:OY8302 4.4 11.6 0.3 O A:HOH405 4.7 20.4 0.5 B15 A:OY8302 4.8 18.2 0.3 OG1 A:THR199 4.8 18.0 1.0 B16 A:OY8302 4.8 17.6 0.3 O3 A:OY5303 4.9 27.7 0.2 N2 A:OY8302 4.9 18.1 0.3 B13 A:OY8302 5.0 17.3 0.3 CD A:GLN92 5.0 13.8 0.4

B.Gruner, M.Kugler, S.El Anwar, J.Holub, J.Nekvinda, D.Bavol, Z.Ruzickova, K.Pospisilova, M.Fabry, V.Kral, J.Brynda, P.Rezacova. Cobalt Bis(Dicarbollide) Alkylsulfonamides: Potent and Highly Selective Inhibitors of Tumor Specific Carbonic Anhydrase IX. Chempluschem 2020.
ISSN: ESSN 2192-6506
PubMed: 32955786
DOI: 10.1002/CPLU.202000574