Zinc in PDB 6ijl: Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5

All present enzymatic activity of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5:
2.1.1.43;

The structure of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5, PDB code: 6ijl was solved by N.Baburajendran, J.Joy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.71 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.212, 66.232, 107.397, 90.00, 90.00, 90.00
R / Rfree (%)	28.1 / 31.6

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5 (pdb code 6ijl). 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 5, PDB code: 6ijl:
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 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:43.1 occ:1.00 CB A:CYS71 2.3 45.2 1.0 SG A:CYS52 2.3 31.1 1.0 SG A:CYS49 2.3 39.2 1.0 SG A:CYS75 2.3 26.7 1.0 CB A:CYS49 3.1 30.5 1.0 SG A:CYS71 3.3 79.1 1.0 CB A:CYS75 3.3 31.1 1.0 CB A:CYS52 3.4 26.6 1.0 N A:CYS52 3.5 27.0 1.0 CA A:CYS71 3.6 43.2 1.0 N A:CYS71 3.7 42.3 1.0 CA A:CYS52 4.0 26.1 1.0 CB A:ARG51 4.2 31.4 1.0 C A:ARG51 4.5 28.1 1.0 CA A:CYS49 4.6 30.3 1.0 C A:CYS71 4.6 40.6 1.0 CA A:CYS75 4.7 30.8 1.0 C A:CYS52 4.8 25.4 1.0 CA A:ARG51 4.8 29.8 1.0 OG A:SER72 4.8 35.1 1.0 N A:SER72 4.8 37.3 1.0 N A:LEU53 4.8 26.2 1.0 N A:ARG51 4.8 30.4 1.0 CG A:ARG51 4.9 32.0 1.0 C A:TYR70 5.0 40.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:28.6 occ:1.00 SG A:CYS208 2.3 32.4 1.0 SG A:CYS263 2.3 28.0 1.0 SG A:CYS266 2.3 29.0 1.0 SG A:CYS261 2.3 26.7 1.0 CB A:CYS263 3.2 27.1 1.0 CB A:CYS208 3.3 22.2 1.0 CB A:CYS261 3.6 23.6 1.0 CB A:CYS266 3.6 22.8 1.0 N A:CYS263 4.0 26.8 1.0 N A:CYS266 4.0 22.5 1.0 CA A:CYS263 4.1 27.1 1.0 N A:CYS208 4.1 22.6 1.0 NH2 A:ARG249 4.3 15.0 1.0 CA A:CYS208 4.3 22.4 1.0 CA A:CYS266 4.4 23.2 1.0 C A:CYS263 4.6 26.6 1.0 C A:CYS261 4.6 24.6 1.0 NE A:ARG249 4.7 15.0 1.0 O A:CYS261 4.7 24.5 1.0 O A:CYS263 4.7 26.6 1.0 NE2 A:HIS206 4.7 18.9 1.0 CA A:CYS261 4.7 23.7 1.0 CZ A:ARG249 5.0 14.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:50.9 occ:1.00 NE2 A:HIS83 2.0 34.4 1.0 SG A:CYS87 2.3 55.7 1.0 SG A:CYS65 2.3 84.2 1.0 SG A:CYS62 2.3 33.0 1.0 CB A:CYS65 2.7 53.4 1.0 CE1 A:HIS83 2.8 33.6 1.0 CB A:CYS62 2.8 34.0 1.0 CD2 A:HIS83 3.1 34.2 1.0 N A:CYS65 3.5 49.4 1.0 CA A:CYS65 3.7 52.9 1.0 CB A:CYS87 3.7 36.6 1.0 ND1 A:HIS83 4.0 33.0 1.0 CG A:HIS83 4.1 33.3 1.0 O A:HOH673 4.3 29.5 1.0 CA A:CYS62 4.3 35.3 1.0 CA A:CYS87 4.4 35.4 1.0 N A:ARG66 4.5 46.0 1.0 CB A:GLN64 4.5 43.9 1.0 CB A:ALA68 4.6 37.4 1.0 C A:GLN64 4.6 47.2 1.0 C A:CYS65 4.7 49.4 1.0 C A:CYS62 4.7 36.3 1.0 O A:CYS62 4.7 35.7 1.0 N A:ALA68 4.8 38.5 1.0 CD1 A:LEU90 5.0 39.6 1.0 CA A:GLN64 5.0 44.4 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