Zinc in PDB 5ccl: Crystal Structure of SMYD3 with Sam and Oxindole Compound

All present enzymatic activity of Crystal Structure of SMYD3 with Sam and Oxindole Compound:
2.1.1.43;

The structure of Crystal Structure of SMYD3 with Sam and Oxindole Compound, PDB code: 5ccl was solved by P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.55 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.594, 65.232, 105.966, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 16.4

The binding sites of Zinc atom in the Crystal Structure of SMYD3 with Sam and Oxindole Compound (pdb code 5ccl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of SMYD3 with Sam and Oxindole Compound, PDB code: 5ccl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SMYD3 with Sam and Oxindole Compound


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 with Sam and Oxindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.1 occ:1.00 SG A:CYS52 2.3 15.9 1.0 SG A:CYS71 2.3 17.8 1.0 SG A:CYS75 2.3 16.7 1.0 SG A:CYS49 2.3 14.8 1.0 CB A:CYS49 3.1 14.0 1.0 CB A:CYS75 3.2 15.1 1.0 CB A:CYS52 3.3 15.6 1.0 CB A:CYS71 3.5 18.1 1.0 N A:CYS52 3.7 13.1 1.0 O A:HOH997 3.9 22.1 1.0 N A:CYS71 3.9 15.8 1.0 CA A:CYS52 4.1 15.1 1.0 O A:HOH962 4.1 22.6 1.0 CA A:CYS71 4.3 17.2 1.0 OG A:SER72 4.4 16.6 1.0 CA A:CYS49 4.6 14.3 1.0 CA A:CYS75 4.6 15.0 1.0 CB A:ARG51 4.7 14.4 0.5 CB A:ARG51 4.8 16.8 0.5 C A:ARG51 4.8 15.6 0.5 C A:ARG51 4.9 15.5 0.5 C A:CYS52 4.9 14.8 1.0 NE A:ARG51 4.9 33.0 0.5 C A:CYS71 4.9 17.3 1.0 N A:SER72 5.0 15.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SMYD3 with Sam and Oxindole Compound


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 with Sam and Oxindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:12.7 occ:1.00 SG A:CYS266 2.3 12.8 1.0 SG A:CYS263 2.3 13.6 1.0 SG A:CYS261 2.3 12.1 1.0 SG A:CYS208 2.4 12.1 1.0 CB A:CYS261 3.3 13.3 1.0 CB A:CYS208 3.3 12.2 1.0 CB A:CYS263 3.4 13.2 1.0 CB A:CYS266 3.4 12.9 1.0 N A:CYS263 4.0 12.8 1.0 N A:CYS208 4.0 10.9 1.0 N A:CYS266 4.0 12.8 1.0 CA A:CYS263 4.2 12.7 1.0 CA A:CYS266 4.3 13.1 1.0 CA A:CYS208 4.3 10.7 1.0 NE2 A:HIS206 4.4 11.3 1.0 CA A:CYS261 4.6 12.6 1.0 O A:CYS263 4.6 12.4 1.0 NH2 A:ARG249 4.6 14.8 1.0 C A:CYS261 4.6 13.4 1.0 C A:CYS263 4.6 12.4 1.0 NE A:ARG249 4.7 12.8 1.0 O A:CYS261 4.8 15.0 1.0 CD2 A:HIS206 4.8 10.3 1.0 O A:HOH949 4.9 18.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SMYD3 with Sam and Oxindole Compound


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 with Sam and Oxindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:18.8 occ:0.50 ZN A:ZN503 0.0 18.8 0.5 SG A:CYS65 1.1 15.8 0.5 ZN A:ZN503 1.4 21.2 0.5 NE2 A:HIS83 2.2 24.4 1.0 SG A:CYS87 2.2 22.3 0.5 SG A:CYS62 2.3 19.9 0.5 CB A:CYS65 2.3 17.0 0.5 SG A:CYS65 2.4 20.0 0.5 SG A:CYS62 2.8 20.1 0.5 SG A:CYS87 3.1 23.5 0.5 N A:CYS65 3.1 27.8 0.5 CE1 A:HIS83 3.1 27.2 1.0 CB A:CYS62 3.1 15.7 0.5 CA A:CYS65 3.2 19.4 0.5 CD2 A:HIS83 3.2 22.5 1.0 CB A:CYS62 3.2 19.3 0.5 CB A:CYS65 3.2 21.9 0.5 CB A:CYS87 3.2 23.3 0.5 N A:CYS65 3.5 19.1 0.5 C A:CYS65 3.8 20.2 0.5 CA A:CYS87 3.9 24.3 0.5 N A:ARG66 3.9 19.8 0.5 CA A:CYS65 3.9 21.6 0.5 CB A:CYS87 4.1 23.6 0.5 N A:VAL67 4.2 23.2 0.5 N A:ALA68 4.2 20.3 0.5 CA A:CYS87 4.2 27.1 0.5 ND1 A:HIS83 4.3 28.5 1.0 CG A:HIS83 4.3 26.0 1.0 C A:GLN64 4.4 27.4 0.5 CB A:GLN64 4.5 30.0 0.5 C A:GLN64 4.5 27.0 0.5 CB A:ALA68 4.5 18.4 0.5 CA A:CYS62 4.5 19.7 0.5 CB A:ALA68 4.6 16.0 0.5 CA A:CYS62 4.6 15.8 0.5 O A:CYS62 4.6 23.3 0.5 O A:CYS65 4.6 21.9 0.5 O A:CYS87 4.7 28.4 0.5 C A:CYS87 4.7 23.9 0.5 C A:CYS62 4.8 23.1 0.5 N A:ARG66 4.8 21.1 0.5 N A:GLN64 4.8 21.6 0.5 O A:CYS87 4.8 25.5 0.5 CA A:GLN64 4.8 28.1 0.5 C A:CYS65 4.9 20.8 0.5 CB A:VAL67 4.9 25.5 0.5 CZ3 A:TRP80 4.9 33.5 1.0 CB A:GLN64 4.9 29.3 0.5 CA A:VAL67 4.9 24.1 0.5 C A:CYS62 4.9 16.5 0.5 C A:CYS87 4.9 26.4 0.5 CA A:ARG66 5.0 20.4 0.5

Zinc binding site 4 out of 4 in the Crystal Structure of SMYD3 with Sam and Oxindole Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SMYD3 with Sam and Oxindole Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:21.2 occ:0.50 ZN A:ZN503 0.0 21.2 0.5 ZN A:ZN503 1.4 18.8 0.5 NE2 A:HIS83 2.0 24.4 1.0 SG A:CYS87 2.3 22.3 0.5 SG A:CYS87 2.3 23.5 0.5 SG A:CYS62 2.3 20.1 0.5 CD2 A:HIS83 2.3 22.5 1.0 SG A:CYS65 2.4 15.8 0.5 SG A:CYS62 2.5 19.9 0.5 CB A:CYS87 2.9 23.3 0.5 CE1 A:HIS83 3.2 27.2 1.0 CB A:CYS65 3.2 17.0 0.5 CB A:CYS87 3.3 23.6 0.5 CB A:CYS62 3.3 19.3 0.5 N A:CYS65 3.5 27.8 0.5 CZ3 A:TRP80 3.5 33.5 1.0 CG A:HIS83 3.6 26.0 1.0 CB A:CYS62 3.7 15.7 0.5 SG A:CYS65 3.7 20.0 0.5 CA A:CYS87 3.9 27.1 0.5 ND1 A:HIS83 4.0 28.5 1.0 CA A:CYS65 4.0 19.4 0.5 CA A:CYS87 4.0 24.3 0.5 O A:HOH651 4.2 41.7 1.0 CE3 A:TRP80 4.3 38.0 1.0 CB A:GLN64 4.3 29.3 0.5 CB A:CYS65 4.5 21.9 0.5 CH2 A:TRP80 4.5 35.4 1.0 N A:CYS65 4.5 19.1 0.5 CB A:GLN64 4.5 30.0 0.5 OE1 A:GLN64 4.6 46.2 0.5 C A:GLN64 4.6 27.4 0.5 O A:HIS83 4.6 28.6 1.0 CA A:CYS62 4.7 19.7 0.5 C A:CYS87 4.8 26.4 0.5 CA A:GLN64 4.8 26.9 0.5 O A:CYS87 4.9 28.4 0.5 C A:CYS65 4.9 20.2 0.5 N A:CYS87 4.9 22.4 0.5 CB A:HIS83 4.9 24.0 1.0 N A:GLN64 4.9 25.2 0.5 CB A:ALA68 4.9 18.4 0.5 N A:CYS87 4.9 28.4 0.5 N A:ARG66 5.0 19.8 0.5

L.H.Mitchell, P.A.Boriack-Sjodin, S.Smith, M.Thomenius, N.Rioux, M.Munchhof, J.E.Mills, C.Klaus, J.Totman, T.V.Riera, A.Raimondi, S.L.Jacques, K.West, M.Foley, N.J.Waters, K.W.Kuntz, T.J.Wigle, M.P.Scott, R.A.Copeland, J.J.Smith, R.Chesworth. Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor. Acs Med.Chem.Lett. V. 7 134 2016.
ISSN: ISSN 1948-5875
PubMed: 26985287
DOI: 10.1021/ACSMEDCHEMLETT.5B00272