Zinc in PDB 5yjo: Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4

All present enzymatic activity of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4:
2.1.1.43;

The structure of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4, PDB code: 5yjo was solved by N.Baburajendran, J.Anna E, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.63 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.428, 66.181, 107.648, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.2

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4 (pdb code 5yjo). 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 in Complex with Covalent Inhibitor 4, PDB code: 5yjo:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4


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 in Complex with Covalent Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.7 occ:1.00 NE2 A:HIS83 2.0 24.0 1.0 SG A:CYS87 2.3 22.5 1.0 SG A:CYS65 2.3 24.0 1.0 SG A:CYS62 2.3 22.4 1.0 CE1 A:HIS83 2.9 21.1 1.0 CD2 A:HIS83 3.2 23.6 1.0 CB A:CYS87 3.2 25.4 1.0 CB A:CYS65 3.2 24.7 1.0 CB A:CYS62 3.2 26.1 1.0 N A:CYS65 3.6 20.9 1.0 CA A:CYS87 3.9 26.3 1.0 CA A:CYS65 4.0 26.7 1.0 ND1 A:HIS83 4.1 22.9 1.0 CG A:HIS83 4.2 21.9 1.0 CB A:GLN64 4.5 31.6 1.0 CA A:CYS62 4.6 28.7 1.0 CB A:ALA68 4.7 26.4 1.0 O A:HOH745 4.7 20.2 1.0 C A:GLN64 4.7 26.2 1.0 CZ3 A:TRP80 4.7 23.2 1.0 C A:CYS87 4.8 27.8 1.0 N A:ARG66 4.8 28.6 1.0 O A:CYS87 4.8 26.6 1.0 C A:CYS65 4.9 24.9 1.0 N A:GLN64 4.9 25.9 1.0 CA A:GLN64 4.9 27.8 1.0 C A:CYS62 4.9 28.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4


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 in Complex with Covalent Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:26.5 occ:1.00 SG A:CYS75 2.3 22.4 1.0 SG A:CYS52 2.3 20.5 1.0 SG A:CYS71 2.4 22.7 1.0 SG A:CYS49 2.4 20.9 1.0 CB A:CYS49 3.1 25.2 1.0 CB A:CYS75 3.2 20.3 1.0 CB A:CYS52 3.4 19.9 1.0 CB A:CYS71 3.5 20.4 1.0 N A:CYS52 3.8 20.4 1.0 N A:CYS71 3.9 24.8 1.0 CA A:CYS52 4.2 24.2 1.0 CA A:CYS71 4.3 26.5 1.0 CA A:CYS49 4.6 23.4 1.0 CA A:CYS75 4.6 21.9 1.0 OG A:SER72 4.7 21.8 1.0 CB A:ARG51 4.7 21.9 1.0 N A:SER72 4.8 25.3 1.0 C A:CYS71 4.9 25.1 1.0 C A:CYS52 4.9 21.3 1.0 C A:ARG51 4.9 21.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 4


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 in Complex with Covalent Inhibitor 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:22.6 occ:1.00 SG A:CYS261 2.3 22.9 1.0 SG A:CYS208 2.3 16.7 1.0 SG A:CYS263 2.3 20.4 1.0 SG A:CYS266 2.3 19.9 1.0 CB A:CYS208 3.3 18.5 1.0 CB A:CYS261 3.3 22.4 1.0 CB A:CYS263 3.4 24.0 1.0 CB A:CYS266 3.5 15.6 1.0 N A:CYS266 4.0 18.1 1.0 N A:CYS263 4.1 27.8 1.0 N A:CYS208 4.3 19.0 1.0 CA A:CYS263 4.3 28.2 1.0 CA A:CYS266 4.4 19.9 1.0 CA A:CYS208 4.4 15.9 1.0 NE A:ARG249 4.6 16.5 1.0 CA A:CYS261 4.6 22.6 1.0 NH2 A:ARG249 4.6 17.5 1.0 C A:CYS261 4.7 22.6 1.0 NE2 A:HIS206 4.7 16.0 1.0 C A:CYS263 4.8 22.5 1.0 O A:CYS261 4.8 21.9 1.0 O A:CYS263 4.8 19.3 1.0 CB A:ARG265 4.9 17.3 1.0

C.Huang, S.S.Liew, G.R.Lin, A.Poulsen, M.J.Y.Ang, B.C.S.Chia, S.Y.Chew, Z.P.Kwek, J.L.K.Wee, E.H.Ong, P.Retna, N.Baburajendran, R.Li, W.Yu, X.Koh-Stenta, A.Ngo, S.Manesh, J.Fulwood, Z.Ke, H.H.Chung, S.Sepramaniam, X.H.Chew, N.Dinie, M.A.Lee, Y.S.Chew, C.B.Low, V.Pendharkar, V.Manoharan, S.Vuddagiri, K.Sangthongpitag, J.Joy, A.Matter, J.Hill, T.H.Keller, K.Foo. Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. Acs Med.Chem.Lett. V. 10 978 2019.
ISSN: ISSN 1948-5875
PubMed: 31223458
DOI: 10.1021/ACSMEDCHEMLETT.9B00170