Zinc in PDB 6p7z: Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors

All present enzymatic activity of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors:
2.1.1.43;

The structure of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors, PDB code: 6p7z was solved by P.A.Elkins, W.G.Bonnette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.62 / 1.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.140, 66.179, 107.330, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.8

The structure of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors (pdb code 6p7z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors, PDB code: 6p7z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.8 occ:1.00 SG A:CYS263 2.3 14.3 1.0 SG A:CYS261 2.3 15.4 1.0 SG A:CYS266 2.3 8.4 1.0 SG A:CYS208 2.3 9.4 1.0 CB A:CYS261 3.3 8.9 1.0 CB A:CYS263 3.4 15.7 1.0 CB A:CYS208 3.4 9.7 1.0 CB A:CYS266 3.4 11.3 1.0 N A:CYS266 4.0 8.4 1.0 N A:CYS263 4.0 17.6 1.0 CA A:CYS263 4.2 14.9 1.0 N A:CYS208 4.3 7.0 1.0 CA A:CYS266 4.3 8.2 1.0 CA A:CYS208 4.5 6.9 1.0 CA A:CYS261 4.5 13.2 1.0 NH2 A:ARG249 4.5 8.0 1.0 C A:CYS261 4.6 14.7 1.0 NE A:ARG249 4.6 7.8 1.0 NE2 A:HIS206 4.7 6.3 1.0 C A:CYS263 4.7 16.0 1.0 O A:CYS261 4.7 13.0 1.0 O A:CYS263 4.8 14.0 1.0 N A:ASP262 5.0 20.2 1.0 CB A:ARG265 5.0 8.1 1.0 O A:HOH989 5.0 10.7 1.0

Zinc binding site 2 out of 3 in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:12.3 occ:1.00 NE2 A:HIS83 2.0 11.5 1.0 SG A:CYS87 2.3 13.8 1.0 SG A:CYS62 2.3 13.7 1.0 SG A:CYS65 2.3 14.1 1.0 CE1 A:HIS83 2.9 11.2 1.0 CD2 A:HIS83 3.1 12.9 1.0 CB A:CYS62 3.2 13.2 1.0 CB A:CYS87 3.2 13.6 1.0 CB A:CYS65 3.2 16.4 1.0 N A:CYS65 3.6 14.2 1.0 CA A:CYS87 3.9 11.9 1.0 CA A:CYS65 4.0 15.7 1.0 ND1 A:HIS83 4.1 10.7 1.0 CG A:HIS83 4.2 10.9 1.0 CB A:GLN64 4.5 16.8 1.0 CA A:CYS62 4.6 13.6 1.0 CZ3 A:TRP80 4.6 14.6 1.0 C A:GLN64 4.6 15.5 1.0 CB A:ALA68 4.6 14.9 1.0 O A:HOH997 4.7 14.5 1.0 C A:CYS87 4.8 17.1 1.0 N A:GLN64 4.8 14.8 1.0 C A:CYS65 4.9 15.0 1.0 N A:ARG66 4.9 14.5 1.0 CA A:GLN64 4.9 15.5 1.0 O A:CYS87 4.9 18.1 1.0 C A:CYS62 4.9 14.4 1.0 O A:CYS62 5.0 14.5 1.0

Zinc binding site 3 out of 3 in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:66.5 occ:1.00 SG A:CYS52 2.3 14.4 1.0 SG A:CYS75 2.3 12.4 1.0 SG A:CYS71 2.3 16.3 1.0 SG A:CYS49 2.3 11.3 1.0 CB A:CYS75 3.1 11.3 1.0 CB A:CYS49 3.2 13.2 1.0 CB A:CYS52 3.3 11.2 1.0 CB A:CYS71 3.5 13.8 1.0 N A:CYS52 3.8 11.1 1.0 O A:HOH1144 3.9 23.1 1.0 N A:CYS71 3.9 14.1 1.0 CA A:CYS52 4.1 11.4 1.0 CA A:CYS71 4.3 15.3 1.0 O A:HOH1025 4.3 23.3 1.0 OG A:SER72 4.4 14.6 1.0 CB A:ARG51 4.6 13.2 0.4 CA A:CYS75 4.6 11.4 1.0 CA A:CYS49 4.6 11.8 1.0 CB A:ARG51 4.7 13.2 0.6 N A:SER72 4.9 14.8 1.0 C A:ARG51 4.9 11.5 1.0 C A:CYS71 4.9 17.1 1.0 C A:CYS52 4.9 11.8 1.0

D.-S.Su, J.Qu, M.Schultz, C.W.Blackledge, H.Yu, J.Zeng, J.Burgess, A.Reif, M.Stern, R.Nagarajan, M.Baker Pappalardi, K.Wong, A.P.Graves, W.Bonnette, L.Wang, P.A.Elkins, B.Knapp-Reed, J.Carson, C.Mchugh, H.Mohammad, R.Kruger, J.Luengo, D.A.Heerding, C.L.Creasy. Discovery of Isoxazone Amides As Potent and Selective SMYD3 Inhibitors Acs Med.Chem.Lett. 2019.
ISSN: ISSN 1948-5875