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Zinc in PDB 4ynd: The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

Enzymatic activity of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

All present enzymatic activity of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2:
2.1.1.43;

Protein crystallography data

The structure of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2, PDB code: 4ynd was solved by R.F.Sweis, Z.Wang, M.Algire, C.H.Arrowsmith, P.J.Brown, G.C.Chiang, J.Guo, C.G.Jakob, S.Kennedy, F.Li, N.B.Soni, M.Vedadi, W.N.Pappano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.67 / 2.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.796, 71.301, 118.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.3

Other elements in 4ynd:

The structure of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 (pdb code 4ynd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2, PDB code: 4ynd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ynd

Go back to Zinc Binding Sites List in 4ynd
Zinc binding site 1 out of 3 in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:36.1
occ:1.00
SG A:CYS78 2.3 36.5 1.0
SG A:CYS55 2.3 27.8 1.0
SG A:CYS52 2.4 28.0 1.0
SG A:CYS74 2.6 33.7 1.0
CB A:CYS74 3.0 29.8 1.0
CB A:CYS52 3.3 24.1 1.0
CB A:CYS78 3.3 32.6 1.0
CB A:CYS55 3.7 24.0 1.0
N A:CYS74 3.7 29.4 1.0
N A:CYS55 4.0 23.9 1.0
CA A:CYS74 4.0 29.6 1.0
CA A:CYS55 4.4 23.7 1.0
CA A:CYS78 4.7 32.3 1.0
O A:HOH632 4.7 27.4 1.0
CB A:TYR54 4.7 24.8 1.0
CA A:CYS52 4.8 23.7 1.0
C A:TYR73 4.9 32.3 1.0
C A:TYR54 5.0 27.4 1.0

Zinc binding site 2 out of 3 in 4ynd

Go back to Zinc Binding Sites List in 4ynd
Zinc binding site 2 out of 3 in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:32.6
occ:1.00
SG A:CYS267 2.3 31.6 1.0
SG A:CYS209 2.3 26.7 1.0
SG A:CYS262 2.4 29.8 1.0
SG A:CYS264 2.5 30.8 1.0
CB A:CYS209 3.1 22.8 1.0
CB A:CYS262 3.3 25.9 1.0
CB A:CYS267 3.3 27.8 1.0
N A:CYS209 3.6 22.4 1.0
CB A:CYS264 3.7 27.0 1.0
CA A:CYS209 4.0 22.4 1.0
N A:CYS267 4.1 27.9 1.0
N A:CYS264 4.2 26.9 1.0
CA A:CYS267 4.2 27.6 1.0
C A:CYS262 4.4 29.8 1.0
CA A:CYS262 4.4 25.6 1.0
CA A:CYS264 4.4 26.8 1.0
NE2 A:HIS207 4.5 25.0 1.0
O A:CYS262 4.6 29.3 1.0
NH2 A:ARG250 4.6 31.8 1.0
NE A:ARG250 4.6 33.4 1.0
C A:SER208 4.7 25.3 1.0
N A:GLU263 4.9 26.8 1.0
C A:CYS264 4.9 31.2 1.0
O A:CYS264 4.9 30.7 1.0
CD2 A:HIS207 5.0 25.2 1.0

Zinc binding site 3 out of 3 in 4ynd

Go back to Zinc Binding Sites List in 4ynd
Zinc binding site 3 out of 3 in the The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:36.1
occ:1.00
NE2 A:HIS86 2.2 31.6 1.0
SG A:CYS68 2.3 34.2 1.0
SG A:CYS90 2.3 35.5 1.0
SG A:CYS65 2.4 34.8 1.0
CE1 A:HIS86 3.0 31.3 1.0
CB A:CYS65 3.2 30.9 1.0
CB A:CYS90 3.3 31.6 1.0
CB A:CYS68 3.4 30.4 1.0
CD2 A:HIS86 3.4 31.9 1.0
N A:CYS68 3.7 30.7 1.0
CA A:CYS90 3.9 31.2 1.0
CA A:CYS68 4.1 30.2 1.0
ND1 A:HIS86 4.2 32.0 1.0
CG A:HIS86 4.4 30.3 1.0
CB A:ARG67 4.6 31.1 1.0
CA A:CYS65 4.7 30.7 1.0
CB A:ALA71 4.7 28.7 1.0
C A:CYS90 4.8 35.7 1.0
N A:LYS69 4.8 30.3 1.0
O A:CYS90 4.8 35.2 1.0
C A:ARG67 4.8 34.5 1.0
N A:CYS90 4.9 31.1 1.0
C A:CYS68 5.0 33.8 1.0
N A:ARG67 5.0 31.0 1.0

Reference:

R.F.Sweis, Z.Wang, M.Algire, C.H.Arrowsmith, P.J.Brown, G.C.Chiang, J.Guo, C.G.Jakob, S.Kennedy, F.Li, N.B.Soni, M.Vedadi, W.N.Pappano. The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 Acs Med.Chem.Lett. 2015.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACSMEDCHEMLETT.5B00124
Page generated: Wed Dec 16 05:57:44 2020

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