Zinc in PDB 7o2a: X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15

All present enzymatic activity of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15:
2.1.1.354;

The structure of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15, PDB code: 7o2a was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.724, 66.191, 107.642, 90, 90, 90
R / Rfree (%)	18.9 / 21.8

The binding sites of Zinc atom in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15 (pdb code 7o2a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15, PDB code: 7o2a:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:9.9 occ:1.00 SG A:CYS266 2.3 7.8 1.0 SG A:CYS261 2.3 12.1 1.0 SG A:CYS263 2.4 9.6 1.0 SG A:CYS208 2.4 9.8 1.0 CB A:CYS261 3.3 9.9 1.0 CB A:CYS266 3.4 8.2 1.0 CB A:CYS208 3.4 8.7 1.0 CB A:CYS263 3.5 8.7 1.0 O A:HOH1433 3.6 22.1 1.0 N A:CYS266 4.0 8.3 1.0 N A:CYS263 4.2 9.5 1.0 CA A:CYS266 4.3 8.5 1.0 CA A:CYS263 4.3 9.4 1.0 NH2 A:ARG249 4.5 7.6 1.0 N A:CYS208 4.5 7.6 1.0 CA A:CYS261 4.6 9.6 1.0 NE A:ARG249 4.6 7.1 1.0 CA A:CYS208 4.6 7.6 1.0 C A:CYS261 4.6 10.4 1.0 O A:CYS261 4.8 10.6 1.0 C A:CYS263 4.8 8.9 1.0 CB A:ARG265 4.9 7.2 1.0 O A:CYS263 4.9 9.7 1.0 O A:HOH1457 4.9 8.2 1.0 NE2 A:HIS206 5.0 5.4 1.0 C A:ARG265 5.0 7.7 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:17.1 occ:1.00 NE2 A:HIS83 2.2 15.5 1.0 SG A:CYS62 2.2 15.6 1.0 SG A:CYS65 2.3 20.1 1.0 SG A:CYS87 2.3 19.9 1.0 CE1 A:HIS83 3.1 14.1 1.0 CB A:CYS62 3.1 16.9 1.0 CD2 A:HIS83 3.2 16.8 1.0 CB A:CYS65 3.2 19.5 1.0 CB A:CYS87 3.3 20.4 1.0 N A:CYS65 3.5 21.4 1.0 CA A:CYS87 3.9 20.4 1.0 CA A:CYS65 3.9 21.4 1.0 ND1 A:HIS83 4.2 14.8 1.0 CG A:HIS83 4.3 15.0 1.0 CB A:GLN64 4.5 30.4 1.0 C A:GLN64 4.6 25.2 1.0 CA A:CYS62 4.6 17.6 1.0 CB A:ALA68 4.6 17.1 1.0 CZ3 A:TRP80 4.8 19.4 1.0 O A:HOH1458 4.8 19.2 1.0 C A:CYS87 4.8 19.0 1.0 C A:CYS65 4.8 24.1 1.0 N A:ARG66 4.8 22.6 1.0 O A:CYS87 4.8 18.5 1.0 CA A:GLN64 4.9 27.0 1.0 N A:GLN64 4.9 25.0 1.0 C A:CYS62 4.9 19.5 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor Compound 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:13.8 occ:1.00 SG A:CYS71 2.3 14.2 1.0 SG A:CYS75 2.3 12.1 1.0 SG A:CYS52 2.3 13.2 1.0 SG A:CYS49 2.4 13.8 1.0 CB A:CYS49 3.2 12.7 1.0 CB A:CYS75 3.2 12.1 1.0 CB A:CYS52 3.3 13.4 1.0 CB A:CYS71 3.4 14.3 1.0 N A:CYS52 3.7 13.1 1.0 O A:HOH1583 3.8 20.5 1.0 N A:CYS71 3.9 16.3 1.0 CA A:CYS52 4.1 13.2 1.0 CA A:CYS71 4.2 15.9 1.0 OG A:SER72 4.3 14.1 1.0 O A:HOH1490 4.4 28.3 1.0 CA A:CYS75 4.7 12.0 1.0 CA A:CYS49 4.7 13.4 1.0 CB A:ARG51 4.7 14.2 0.5 CB A:ARG51 4.8 14.9 0.5 N A:SER72 4.9 14.0 1.0 C A:ARG51 4.9 14.2 1.0 C A:CYS71 4.9 16.6 1.0 C A:CYS52 5.0 13.3 1.0

S.Gradl, H.Steuber, J.Weiske, M.M.Szewczyk, N.Schmees, S.Siegel, D.Stoeckigt, C.D.Christ, F.Li, S.Organ, M.Abbey, S.Kennedy, I.Chau, V.Trush, D.Barsyte-Lovejoy, P.J.Brown, M.Vedadi, C.Arrowsmith, M.Husemann, V.Badock, M.Bauser, A.Haegebarth, I.V.Hartung, C.Stresemann. Discovery of the SMYD3 Inhibitor Bay-6035 Using Thermal Shift Assay (Tsa)-Based High-Throughput Screening. Slas Discov 19409 2021.
ISSN: ISSN 2472-5560
PubMed: 34154424
DOI: 10.1177/24725552211019409