Zinc in PDB 6p6g: 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: 6p6g 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)	56.61 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.433, 66.636, 107.340, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20

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

Fluorine	(F)	3 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors (pdb code 6p6g). 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: 6p6g:
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:17.5 occ:1.00 SG A:CYS261 2.3 20.1 1.0 SG A:CYS263 2.3 19.5 1.0 SG A:CYS266 2.3 15.7 1.0 SG A:CYS208 2.4 17.8 1.0 CB A:CYS208 3.4 16.3 1.0 CB A:CYS266 3.4 14.7 1.0 CB A:CYS261 3.4 16.7 1.0 CB A:CYS263 3.4 21.2 1.0 N A:CYS263 4.0 21.3 1.0 N A:CYS266 4.0 14.8 1.0 CA A:CYS263 4.2 17.1 1.0 N A:CYS208 4.2 16.6 1.0 CA A:CYS266 4.3 15.5 1.0 CA A:CYS208 4.4 15.3 1.0 C A:CYS261 4.5 20.5 1.0 CA A:CYS261 4.6 19.3 1.0 O A:CYS261 4.6 19.7 1.0 NH2 A:ARG249 4.6 15.4 1.0 NE2 A:HIS206 4.6 12.2 1.0 NE A:ARG249 4.6 16.0 1.0 C A:CYS263 4.6 18.9 1.0 O A:CYS263 4.7 18.1 1.0 N A:ASP262 5.0 20.8 1.0 O A:HOH882 5.0 18.9 1.0 CB A:ARG265 5.0 16.1 1.0 CD2 A:HIS206 5.0 13.4 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:23.7 occ:1.00 NE2 A:HIS83 2.1 22.2 1.0 SG A:CYS62 2.3 22.7 1.0 SG A:CYS87 2.3 23.8 1.0 SG A:CYS65 2.4 25.9 1.0 CE1 A:HIS83 3.1 23.0 1.0 CD2 A:HIS83 3.1 20.0 1.0 CB A:CYS62 3.2 23.0 1.0 CB A:CYS65 3.2 24.8 1.0 CB A:CYS87 3.2 23.7 1.0 N A:CYS65 3.5 25.5 1.0 CA A:CYS87 3.9 26.8 1.0 CA A:CYS65 4.0 29.6 1.0 ND1 A:HIS83 4.2 22.0 1.0 CG A:HIS83 4.2 21.4 1.0 CB A:GLN64 4.4 29.0 1.0 C A:GLN64 4.6 32.1 1.0 CA A:CYS62 4.6 24.4 1.0 CZ3 A:TRP80 4.6 24.0 1.0 CB A:ALA68 4.6 25.2 1.0 O A:HOH913 4.7 24.3 1.0 N A:GLN64 4.8 27.8 1.0 N A:ARG66 4.8 26.7 1.0 C A:CYS87 4.8 24.7 1.0 CA A:GLN64 4.8 27.2 1.0 C A:CYS65 4.8 27.8 1.0 C A:CYS62 4.9 26.8 1.0 O A:CYS87 4.9 26.7 1.0 O A:CYS62 5.0 25.9 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:23.1 occ:1.00 SG A:CYS75 2.2 23.8 1.0 SG A:CYS52 2.3 21.8 1.0 SG A:CYS71 2.3 23.2 1.0 SG A:CYS49 2.5 22.4 1.0 CB A:CYS75 3.2 25.1 1.0 CB A:CYS49 3.2 23.1 1.0 CB A:CYS52 3.3 24.2 1.0 CB A:CYS71 3.3 17.1 1.0 N A:CYS52 3.7 18.8 1.0 N A:CYS71 4.0 24.8 1.0 CA A:CYS52 4.1 18.9 1.0 CA A:CYS71 4.3 27.1 1.0 O A:HOH920 4.4 33.6 1.0 OG A:SER72 4.5 25.5 1.0 CA A:CYS75 4.6 23.4 1.0 CB A:ARG51 4.7 21.3 1.0 CA A:CYS49 4.7 20.3 1.0 C A:ARG51 4.9 22.8 1.0 C A:CYS52 4.9 19.6 1.0 C A:CYS71 5.0 29.6 1.0 N A:SER72 5.0 21.1 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