Zinc in PDB 8qtk: Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)

The structure of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31), PDB code: 8qtk was solved by M.Schimpl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.48 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.268, 74.966, 97.56, 90, 90, 90
R / Rfree (%)	20.9 / 26.8

The structure of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) (pdb code 8qtk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31), PDB code: 8qtk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.2 occ:1.00 SG A:CYS373 2.2 38.9 1.0 SG A:CYS393 2.3 39.1 1.0 SG A:CYS396 2.4 35.3 1.0 SG A:CYS376 2.5 40.4 1.0 CB A:CYS373 3.0 41.3 1.0 CB A:CYS396 3.2 37.5 1.0 CB A:CYS376 3.4 39.3 1.0 CB A:CYS393 3.5 39.1 1.0 N A:CYS376 3.7 40.3 1.0 N A:CYS393 3.9 39.5 1.0 CA A:CYS393 4.2 39.3 1.0 CA A:CYS376 4.2 39.9 1.0 N A:CYS396 4.3 39.8 1.0 CA A:CYS396 4.3 38.7 1.0 CA A:CYS373 4.4 41.5 1.0 CB A:ILE375 4.5 40.3 1.0 O A:CYS393 4.5 38.3 1.0 ND2 A:ASN379 4.6 43.5 1.0 CB A:ASN379 4.7 42.1 1.0 C A:CYS393 4.7 39.2 1.0 C A:ILE375 4.7 41.4 1.0 C A:CYS373 4.8 41.2 1.0 O A:ASN379 4.8 40.4 1.0 N A:ILE375 4.9 40.3 1.0 O A:CYS373 4.9 40.5 1.0 CA A:ILE375 4.9 40.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cbl-B in Complex with An Allosteric Inhibitor (Compound 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:51.0 occ:1.00 ND1 A:HIS390 1.9 58.9 1.0 SG A:CYS388 2.3 54.2 1.0 SG A:CYS411 2.4 58.8 1.0 SG A:CYS408 2.4 54.8 1.0 CE1 A:HIS390 2.8 59.5 1.0 CG A:HIS390 3.0 56.2 1.0 CB A:CYS408 3.1 55.6 1.0 CB A:CYS388 3.2 54.7 1.0 CB A:CYS411 3.5 61.1 1.0 CB A:HIS390 3.5 50.8 1.0 N A:CYS411 3.9 61.0 1.0 NE2 A:HIS390 4.0 59.7 1.0 CD2 A:HIS390 4.1 58.2 1.0 CA A:CYS411 4.2 62.0 1.0 CB A:PHE410 4.4 59.0 1.0 N A:HIS390 4.5 48.6 1.0 CA A:CYS388 4.5 54.1 1.0 CA A:HIS390 4.6 48.4 1.0 CA A:CYS408 4.6 56.3 1.0 C A:PHE410 4.8 60.5 1.0 C A:CYS388 4.8 53.6 1.0 N A:ARG412 4.9 65.7 1.0 C A:CYS411 4.9 64.4 1.0 CA A:PHE410 5.0 59.5 1.0 N A:PHE410 5.0 58.8 1.0

A.M.Mfuh, J.A.Boerth, G.Bommakanti, C.Chan, A.J.Chinn, E.Code, P.J.Fricke, K.A.Giblin, A.Gohlke, C.Hansel, N.Hariparsad, S.J.Hughes, M.Jin, V.Kantae, S.L.Kavanagh, M.L.Lamb, J.Lane, R.Moore, T.Puri, T.R.Quinn, I.Reddy, G.R.Robb, K.J.Robbins, M.Gancedo Rodrigo, M.Schimpl, B.Singh, M.Singh, H.Tang, C.Thomson, J.J.Walsh, J.Ware, I.D.G.Watson, M.W.Ye, G.L.Wrigley, A.X.Zhang, Y.Zhang, N.P.Grimster. Discovery, Optimization, and Biological Evaluation of Arylpyridones As Cbl-B Inhibitors. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38227216
DOI: 10.1021/ACS.JMEDCHEM.3C02083