Zinc in PDB 6zrb: Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127

All present enzymatic activity of Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127:
2.1.1.354;

The structure of Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127, PDB code: 6zrb was solved by V.O.Talibov, D.Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.28 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.935, 65.989, 107.318, 90, 90, 90
R / Rfree (%)	16.5 / 18.5

The binding sites of Zinc atom in the Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127 (pdb code 6zrb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127, PDB code: 6zrb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:16.8 occ:1.00 SG A:CYS263 2.3 18.6 1.0 SG A:CYS266 2.3 15.1 1.0 SG A:CYS261 2.3 18.9 1.0 SG A:CYS208 2.4 16.8 1.0 CB A:CYS261 3.3 17.9 1.0 CB A:CYS263 3.4 20.2 1.0 CB A:CYS208 3.4 15.2 1.0 CB A:CYS266 3.4 15.3 1.0 N A:CYS266 4.0 15.8 1.0 N A:CYS263 4.0 20.4 1.0 CA A:CYS263 4.2 19.4 1.0 N A:CYS208 4.2 14.6 1.0 CA A:CYS266 4.3 15.8 1.0 CA A:CYS208 4.4 14.6 1.0 NE2 A:HIS206 4.5 12.6 1.0 CA A:CYS261 4.5 18.9 1.0 C A:CYS261 4.6 18.0 1.0 NH2 A:ARG249 4.6 14.6 1.0 NE A:ARG249 4.6 14.5 1.0 O A:CYS263 4.7 19.1 1.0 C A:CYS263 4.7 18.1 1.0 O A:CYS261 4.7 19.0 1.0 O A:HOH935 4.9 22.6 1.0 CD2 A:HIS206 5.0 12.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:19.1 occ:1.00 SG A:CYS52 2.3 18.9 1.0 SG A:CYS71 2.3 20.5 1.0 SG A:CYS75 2.3 19.2 1.0 SG A:CYS49 2.4 17.6 1.0 CB A:CYS75 3.1 19.1 1.0 CB A:CYS49 3.1 17.5 1.0 CB A:CYS52 3.3 19.2 1.0 CB A:CYS71 3.4 20.4 1.0 N A:CYS52 3.7 17.7 1.0 O A:HOH1012 3.9 28.0 1.0 N A:CYS71 3.9 21.3 1.0 CA A:CYS52 4.1 18.5 1.0 CA A:CYS71 4.2 21.1 1.0 O A:HOH962 4.2 29.8 1.0 OG A:SER72 4.4 22.3 1.0 CA A:CYS75 4.6 18.1 1.0 CA A:CYS49 4.6 18.0 1.0 CB A:ARG51 4.7 20.8 1.0 C A:ARG51 4.9 18.5 1.0 C A:CYS52 4.9 18.6 1.0 N A:SER72 4.9 20.2 1.0 C A:CYS71 4.9 21.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SMYD3 Conjugate with Piperidine-Based Covalent Inhibitor EM127 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:19.3 occ:1.00 NE2 A:HIS83 2.1 16.1 1.0 SG A:CYS62 2.3 19.2 1.0 SG A:CYS65 2.3 20.6 1.0 SG A:CYS87 2.3 20.4 1.0 CE1 A:HIS83 3.1 16.9 1.0 CD2 A:HIS83 3.1 16.0 1.0 CB A:CYS62 3.1 20.4 1.0 CB A:CYS87 3.2 19.9 1.0 CB A:CYS65 3.3 20.5 1.0 N A:CYS65 3.5 20.7 1.0 CA A:CYS87 3.9 20.6 1.0 CA A:CYS65 4.0 22.1 1.0 ND1 A:HIS83 4.2 16.6 1.0 CG A:HIS83 4.2 16.9 1.0 CB A:GLN64 4.5 26.4 1.0 CA A:CYS62 4.5 20.8 1.0 CB A:ALA68 4.6 18.2 1.0 C A:GLN64 4.6 24.0 1.0 CZ3 A:TRP80 4.7 23.4 1.0 O A:HOH944 4.7 20.0 1.0 C A:CYS87 4.8 22.6 1.0 O A:CYS87 4.8 22.6 1.0 CA A:GLN64 4.8 24.2 1.0 N A:GLN64 4.9 22.7 1.0 N A:ARG66 4.9 21.4 1.0 C A:CYS62 4.9 20.8 1.0 C A:CYS65 4.9 22.2 1.0 O A:CYS62 5.0 20.6 1.0

M.D.Parenti, M.Naldi, E.Manoni, E.Fabini, D.Cederfelt, V.O.Talibov, V.Gressani, U.Guven, V.Grossi, C.Fasano, P.Sanese, K.De Marco, A.A.Shtil, A.V.Kurkin, A.Altieri, U.H.Danielson, G.Caretti, C.Simone, G.Varchi, M.Bartolini, A.Del Rio. Discovery of the 4-Aminopiperidine-Based Compound EM127 For the Site-Specific Covalent Inhibition of SMYD3 Eur.J.Med.Chem. 14683 2022.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2022.114683