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Chlorine in PDB 5kjm: SMYD2 in Complex with AZ931

Enzymatic activity of SMYD2 in Complex with AZ931

All present enzymatic activity of SMYD2 in Complex with AZ931:
2.1.1.43;

Protein crystallography data

The structure of SMYD2 in Complex with AZ931, PDB code: 5kjm was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.02 / 2.19
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 156.033, 156.033, 52.735, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.4

Other elements in 5kjm:

The structure of SMYD2 in Complex with AZ931 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the SMYD2 in Complex with AZ931 (pdb code 5kjm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the SMYD2 in Complex with AZ931, PDB code: 5kjm:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5kjm

Go back to Chlorine Binding Sites List in 5kjm
Chlorine binding site 1 out of 2 in the SMYD2 in Complex with AZ931


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of SMYD2 in Complex with AZ931 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:54.9
occ:1.00
CL1 A:6TM502 0.0 54.9 1.0
C38 A:6TM502 1.7 53.6 1.0
C37 A:6TM502 2.7 52.5 1.0
C39 A:6TM502 2.7 54.8 1.0
CL2 A:6TM502 3.1 61.1 1.0
O A:HOH639 3.7 33.8 1.0
CD1 A:LEU141 3.8 51.1 1.0
CD A:LYS145 3.8 58.5 1.0
CZ A:PHE259 3.9 42.2 1.0
CB A:ASN180 4.0 34.0 1.0
C36 A:6TM502 4.0 52.9 1.0
C40 A:6TM502 4.0 51.2 1.0
CE2 A:PHE259 4.1 43.0 1.0
CD1 A:ILE149 4.1 41.0 1.0
CG A:ASN180 4.1 67.3 1.0
ND2 A:ASN180 4.2 58.9 1.0
CE A:LYS145 4.2 63.6 1.0
CG A:LYS145 4.4 51.8 1.0
C35 A:6TM502 4.5 51.9 1.0
CB A:LYS145 4.5 43.9 1.0
CA A:ALA177 4.7 31.7 1.0
OD1 A:ASN180 4.7 69.8 1.0
CB A:ALA177 4.8 33.2 1.0
CG A:LEU141 4.8 50.9 1.0
CG1 A:ILE149 4.9 41.5 1.0

Chlorine binding site 2 out of 2 in 5kjm

Go back to Chlorine Binding Sites List in 5kjm
Chlorine binding site 2 out of 2 in the SMYD2 in Complex with AZ931


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of SMYD2 in Complex with AZ931 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:61.1
occ:1.00
CL2 A:6TM502 0.0 61.1 1.0
C39 A:6TM502 1.7 54.8 1.0
C40 A:6TM502 2.7 51.2 1.0
C38 A:6TM502 2.7 53.6 1.0
CL1 A:6TM502 3.1 54.9 1.0
CG1 A:ILE149 3.7 41.5 1.0
CD1 A:ILE149 3.8 41.0 1.0
ND2 A:ASN180 3.8 58.9 1.0
O A:LYS145 3.8 44.2 1.0
C35 A:6TM502 4.0 51.9 1.0
C37 A:6TM502 4.0 52.5 1.0
CG A:ASN180 4.1 67.3 1.0
CG A:LYS145 4.1 51.8 1.0
CB A:LYS145 4.1 43.9 1.0
OD1 A:ASN180 4.1 69.8 1.0
CB A:LEU148 4.2 42.9 1.0
CA A:LYS145 4.3 42.3 1.0
C A:LYS145 4.4 45.2 1.0
C36 A:6TM502 4.5 52.9 1.0
CD1 A:LEU148 4.5 49.9 1.0
CD A:LYS145 4.6 58.5 1.0
N A:ILE149 4.7 40.4 1.0
CB A:ILE149 4.9 42.9 1.0
CB A:ASN180 5.0 34.0 1.0
CG A:LEU148 5.0 49.5 1.0

Reference:

S.D.Cowen, D.Russell, L.A.Dakin, H.Chen, N.A.Larsen, R.Godin, S.Throner, X.Zheng, A.Molina, J.Wu, T.Cheung, T.Howard, R.Garcia-Arenas, N.Keen, C.S.Pendleton, J.A.Pietenpol, A.D.Ferguson. Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J. Med. Chem. V. 59 11079 2016.
ISSN: ISSN 1520-4804
PubMed: 28002961
Page generated: Fri Jul 26 10:42:34 2024

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