Zinc in PDB 6paf: 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: 6paf was solved by P.A.Elkins, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.971, 65.991, 106.544, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.8

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 6paf). 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: 6paf:
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:12.2 occ:1.00 SG A:CYS263 2.2 15.7 1.0 SG A:CYS261 2.3 16.8 1.0 SG A:CYS266 2.3 9.6 1.0 SG A:CYS208 2.4 10.3 1.0 CB A:CYS263 3.3 14.8 1.0 CB A:CYS261 3.3 11.1 1.0 CB A:CYS266 3.4 12.8 1.0 CB A:CYS208 3.4 9.7 1.0 N A:CYS263 3.8 15.6 1.0 CA A:CYS263 4.0 12.6 1.0 N A:CYS266 4.0 8.7 1.0 N A:CYS208 4.2 7.6 1.0 CA A:CYS266 4.3 10.1 1.0 CA A:CYS208 4.5 7.7 1.0 C A:CYS261 4.5 19.2 1.0 CA A:CYS261 4.5 15.9 1.0 C A:CYS263 4.5 17.5 1.0 NH2 A:ARG249 4.5 7.8 1.0 O A:CYS263 4.6 16.1 1.0 NE A:ARG249 4.6 9.2 1.0 O A:CYS261 4.6 15.9 1.0 NE2 A:HIS206 4.7 6.8 1.0 N A:ASP262 4.9 19.4 1.0 CB A:ARG265 4.9 9.2 1.0 O A:HOH965 5.0 11.6 1.0 C A:ARG265 5.0 9.4 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:17.8 occ:1.00 NE2 A:HIS83 2.0 19.1 1.0 SG A:CYS65 2.3 21.9 1.0 SG A:CYS62 2.3 22.1 1.0 SG A:CYS87 2.3 21.3 1.0 CE1 A:HIS83 3.0 18.4 1.0 CD2 A:HIS83 3.0 19.6 1.0 CB A:CYS65 3.1 22.6 1.0 CB A:CYS62 3.2 22.1 1.0 CB A:CYS87 3.2 19.9 1.0 N A:CYS65 3.5 25.3 1.0 CA A:CYS65 3.9 26.2 1.0 CA A:CYS87 3.9 19.8 1.0 ND1 A:HIS83 4.1 17.4 1.0 CG A:HIS83 4.2 17.5 1.0 CB A:GLN64 4.4 25.6 1.0 C A:GLN64 4.5 26.8 1.0 CZ3 A:TRP80 4.6 21.4 1.0 CA A:CYS62 4.6 23.3 1.0 CB A:ALA68 4.6 23.8 1.0 O A:HOH984 4.7 18.9 1.0 N A:GLN64 4.8 25.4 1.0 CA A:GLN64 4.8 27.2 1.0 N A:ARG66 4.8 25.9 1.0 C A:CYS87 4.8 23.2 1.0 C A:CYS65 4.8 30.8 1.0 C A:CYS62 4.9 24.6 1.0 O A:CYS87 4.9 23.0 1.0 O A:CYS62 5.0 25.0 1.0 N A:CYS87 5.0 18.7 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:17.0 occ:1.00 SG A:CYS52 2.2 19.8 1.0 SG A:CYS75 2.3 19.1 1.0 SG A:CYS71 2.3 23.9 1.0 SG A:CYS49 2.5 18.3 1.0 CB A:CYS75 3.2 18.9 1.0 CB A:CYS52 3.3 19.0 1.0 CB A:CYS49 3.3 19.0 1.0 CB A:CYS71 3.4 21.8 1.0 N A:CYS52 3.7 16.6 1.0 CA A:CYS52 4.0 16.2 1.0 N A:CYS71 4.1 21.5 1.0 O A:HOH1003 4.2 30.1 1.0 CA A:CYS71 4.3 24.1 1.0 OG A:SER72 4.4 22.2 1.0 CA A:CYS75 4.6 19.0 1.0 CB A:ARG51 4.7 16.3 1.0 CA A:CYS49 4.7 18.7 1.0 C A:ARG51 4.8 18.3 1.0 C A:CYS52 4.8 16.3 1.0 N A:SER72 4.9 22.9 1.0 C A:CYS71 4.9 25.7 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