Zinc in PDB 7o2c: X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035

All present enzymatic activity of X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035:
2.1.1.354;

The structure of X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035, PDB code: 7o2c was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.64 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.497, 66.166, 107.165, 90, 90, 90
R / Rfree (%)	15.8 / 22.5

The binding sites of Zinc atom in the X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035 (pdb code 7o2c). 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 the Benzodiazepine-Based Probe Bay-6035, PDB code: 7o2c:
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 the Benzodiazepine-Based Probe Bay-6035


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 the Benzodiazepine-Based Probe Bay-6035 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:13.2 occ:1.00 SG A:CYS261 2.3 15.9 1.0 SG A:CYS208 2.3 13.7 1.0 SG A:CYS266 2.3 11.5 1.0 SG A:CYS263 2.4 15.8 1.0 CB A:CYS208 3.4 12.2 1.0 CB A:CYS261 3.4 10.6 1.0 CB A:CYS266 3.4 11.3 1.0 O A:HOH997 3.4 32.4 1.0 CB A:CYS263 3.5 13.8 1.0 N A:CYS266 4.0 11.3 1.0 N A:CYS263 4.2 17.2 1.0 CA A:CYS266 4.3 10.6 1.0 CA A:CYS263 4.3 18.1 1.0 N A:CYS208 4.5 9.0 1.0 NH2 A:ARG249 4.6 10.5 1.0 CA A:CYS208 4.6 9.1 1.0 CA A:CYS261 4.6 12.2 1.0 NE A:ARG249 4.6 10.1 1.0 C A:CYS261 4.6 15.2 1.0 O A:CYS261 4.7 14.8 1.0 NE2 A:HIS206 4.8 7.0 1.0 C A:CYS263 4.8 13.7 1.0 O A:CYS263 4.9 15.1 1.0 O A:HOH993 4.9 11.6 1.0 CB A:ARG265 5.0 8.7 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035


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 the Benzodiazepine-Based Probe Bay-6035 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:18.9 occ:1.00 SG A:CYS71 2.3 21.4 1.0 SG A:CYS75 2.3 20.2 1.0 SG A:CYS52 2.3 20.8 1.0 SG A:CYS49 2.4 20.0 1.0 CB A:CYS75 3.1 17.2 1.0 CB A:CYS49 3.2 19.3 1.0 CB A:CYS71 3.3 20.0 1.0 CB A:CYS52 3.3 16.9 1.0 N A:CYS52 3.7 18.9 1.0 O A:HOH1142 3.7 29.3 1.0 N A:CYS71 3.9 23.0 1.0 CA A:CYS52 4.1 18.0 1.0 CA A:CYS71 4.2 24.1 1.0 OG A:SER72 4.3 20.2 1.0 O A:HOH1018 4.4 32.9 1.0 CA A:CYS75 4.5 17.4 1.0 CB A:ARG51 4.7 18.1 0.5 CB A:ARG51 4.7 18.5 0.5 CA A:CYS49 4.7 16.7 1.0 N A:SER72 4.8 20.1 1.0 C A:ARG51 4.8 16.6 1.0 C A:CYS71 4.9 23.3 1.0 C A:CYS52 4.9 17.3 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of SMYD3 in Complex with the Benzodiazepine-Based Probe Bay-6035


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 the Benzodiazepine-Based Probe Bay-6035 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:21.8 occ:1.00 NE2 A:HIS83 2.1 21.5 1.0 SG A:CYS62 2.3 20.6 1.0 SG A:CYS87 2.3 24.6 1.0 SG A:CYS65 2.3 25.1 1.0 CE1 A:HIS83 3.0 17.6 1.0 CD2 A:HIS83 3.1 19.5 1.0 CB A:CYS62 3.2 21.4 1.0 CB A:CYS65 3.2 21.2 1.0 CB A:CYS87 3.3 21.2 1.0 N A:CYS65 3.6 23.5 1.0 CA A:CYS87 3.9 21.0 1.0 CA A:CYS65 4.0 25.3 1.0 ND1 A:HIS83 4.2 19.4 1.0 CG A:HIS83 4.2 18.3 1.0 CB A:GLN64 4.5 32.0 1.0 C A:GLN64 4.6 31.8 1.0 CA A:CYS62 4.6 22.3 1.0 CB A:ALA68 4.7 27.5 1.0 CZ3 A:TRP80 4.7 22.1 1.0 C A:CYS87 4.8 22.6 1.0 CA A:GLN64 4.9 27.4 1.0 O A:HOH991 4.9 21.6 1.0 C A:CYS65 4.9 28.4 1.0 N A:GLN64 4.9 34.3 1.0 O A:CYS87 4.9 24.4 1.0 C A:CYS62 4.9 24.3 1.0 N A:ARG66 5.0 26.7 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