Zinc in PDB 6p6k: 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: 6p6k 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)	31.52 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.719, 66.038, 105.773, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.4

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 6p6k). 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: 6p6k:
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:18.9 occ:1.00 SG A:CYS261 2.2 22.6 1.0 SG A:CYS263 2.2 22.3 1.0 SG A:CYS266 2.3 15.3 1.0 SG A:CYS208 2.4 19.1 1.0 CB A:CYS263 3.3 27.1 1.0 CB A:CYS261 3.4 15.4 1.0 CB A:CYS266 3.4 18.2 1.0 CB A:CYS208 3.4 16.9 1.0 N A:CYS266 4.0 16.1 1.0 N A:CYS263 4.0 33.1 1.0 CA A:CYS263 4.2 25.1 1.0 CA A:CYS266 4.3 21.3 1.0 N A:CYS208 4.3 12.4 1.0 CA A:CYS208 4.5 13.3 1.0 C A:CYS261 4.5 24.3 1.0 CA A:CYS261 4.5 24.1 1.0 NH2 A:ARG249 4.6 13.8 1.0 NE A:ARG249 4.6 15.4 1.0 O A:CYS261 4.7 19.9 1.0 C A:CYS263 4.7 27.8 1.0 NE2 A:HIS206 4.7 13.4 1.0 O A:CYS263 4.7 23.9 1.0 CB A:ARG265 4.9 15.3 1.0 N A:ASP262 4.9 30.2 1.0 O A:HOH894 5.0 20.1 1.0 C A:ARG265 5.0 15.4 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:27.4 occ:1.00 NE2 A:HIS83 2.1 34.5 1.0 SG A:CYS62 2.3 31.8 1.0 SG A:CYS87 2.3 32.1 1.0 SG A:CYS65 2.4 36.4 1.0 CB A:CYS65 3.0 33.0 1.0 CD2 A:HIS83 3.1 30.9 1.0 CE1 A:HIS83 3.1 30.9 1.0 CB A:CYS87 3.2 31.4 1.0 CB A:CYS62 3.3 32.8 1.0 N A:CYS65 3.5 44.6 1.0 CA A:CYS65 3.9 42.9 1.0 CA A:CYS87 3.9 28.9 1.0 ND1 A:HIS83 4.2 26.0 1.0 CG A:HIS83 4.2 28.9 1.0 CB A:GLN64 4.3 37.8 1.0 C A:GLN64 4.5 43.3 1.0 CA A:CYS62 4.6 33.9 1.0 CB A:ALA68 4.7 38.5 1.0 C A:CYS87 4.8 27.6 1.0 O A:HOH902 4.8 29.6 1.0 C A:CYS65 4.8 55.3 1.0 CZ3 A:TRP80 4.8 31.9 1.0 CA A:GLN64 4.8 42.2 1.0 O A:CYS87 4.8 28.6 1.0 N A:ARG66 4.8 57.6 1.0 N A:GLN64 4.9 41.6 1.0 O A:CYS62 4.9 43.2 1.0 C A:CYS62 4.9 37.9 1.0 N A:CYS87 5.0 25.1 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:29.4 occ:1.00 SG A:CYS52 2.3 30.4 1.0 SG A:CYS75 2.3 35.1 1.0 SG A:CYS71 2.3 33.9 1.0 SG A:CYS49 2.6 30.1 1.0 CB A:CYS75 3.1 31.8 1.0 CB A:CYS52 3.2 31.2 1.0 CB A:CYS49 3.3 39.8 1.0 CB A:CYS71 3.4 33.0 1.0 N A:CYS52 3.7 24.3 1.0 CA A:CYS52 4.0 27.3 1.0 N A:CYS71 4.1 35.1 1.0 CA A:CYS71 4.3 37.9 1.0 OG A:SER72 4.3 36.9 1.0 CB A:ARG51 4.5 29.5 0.5 CA A:CYS75 4.5 32.2 1.0 CB A:ARG51 4.7 29.1 0.5 N A:SER72 4.7 38.3 1.0 CA A:CYS49 4.8 35.6 1.0 C A:ARG51 4.8 24.8 1.0 C A:CYS71 4.9 40.6 1.0 C A:CYS52 4.9 28.3 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