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Zinc in PDB 4k4e: Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]

Enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]

All present enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide], PDB code: 4k4e was solved by X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.12 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.440, 73.264, 149.059, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 28

Other elements in 4k4e:

The structure of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] (pdb code 4k4e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide], PDB code: 4k4e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4k4e

Go back to Zinc Binding Sites List in 4k4e
Zinc binding site 1 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:36.8
occ:1.00
 ND1 A:HIS1237 2.2 37.2 1.0
SG A:CYS1242 2.4 29.8 1.0
SG A:CYS1234 2.4 31.9 1.0
SG A:CYS1245 2.5 37.8 1.0
CE1 A:HIS1237 3.0 36.8 1.0
CG A:HIS1237 3.1 36.8 1.0
CB A:CYS1234 3.1 33.4 1.0
CB A:CYS1245 3.4 34.2 1.0
CB A:CYS1242 3.4 29.4 1.0
CB A:HIS1237 3.5 35.6 1.0
N A:CYS1245 3.9 33.6 1.0
N A:HIS1237 3.9 35.4 1.0
NE2 A:HIS1237 4.0 37.9 1.0
CD2 A:HIS1237 4.1 37.8 1.0
CA A:CYS1245 4.3 34.2 1.0
CA A:HIS1237 4.4 34.9 1.0
O A:HOH1522 4.5 34.0 1.0
CB A:THR1236 4.5 36.5 1.0
CA A:CYS1234 4.6 36.1 1.0
CB A:ILE1244 4.6 34.7 1.0
C A:THR1236 4.7 36.0 1.0
CA A:CYS1242 4.8 29.8 1.0
N A:THR1236 5.0 36.6 1.0
CA A:THR1236 5.0 36.3 1.0

Zinc binding site 2 out of 2 in 4k4e

Go back to Zinc Binding Sites List in 4k4e
Zinc binding site 2 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of TNKS1 with Compound 52 [N~2-(5-Chloro-2- Methoxyphenyl)-N-[Trans-4-(2-Oxo-2,3-Dihydro-1H-Benzimidazol-1-Yl) Cyclohexyl]Glycinamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:44.2
occ:1.00
 ND1 B:HIS1237 2.1 52.9 1.0
SG B:CYS1242 2.3 38.0 1.0
SG B:CYS1245 2.4 41.6 1.0
SG B:CYS1234 2.6 46.3 1.0
CE1 B:HIS1237 2.9 53.1 1.0
CG B:HIS1237 3.0 53.0 1.0
CB B:CYS1242 3.4 38.7 1.0
CB B:CYS1245 3.4 39.2 1.0
CB B:HIS1237 3.4 50.7 1.0
CB B:CYS1234 3.5 48.9 1.0
N B:CYS1245 3.8 38.2 1.0
N B:HIS1237 3.9 51.7 1.0
NE2 B:HIS1237 3.9 53.6 1.0
CD2 B:HIS1237 3.9 53.2 1.0
CA B:CYS1245 4.2 37.8 1.0
CA B:HIS1237 4.3 51.5 1.0
CB B:ILE1244 4.6 37.3 1.0
CB B:THR1236 4.7 52.2 1.0
C B:THR1236 4.7 51.9 1.0
CA B:CYS1242 4.8 39.1 1.0
CA B:CYS1234 4.9 49.9 1.0
C B:ILE1244 4.9 38.0 1.0
CB B:ASP1239 4.9 51.1 1.0

Reference:

H.Bregman, N.Chakka, A.Guzman-Perez, H.Gunaydin, Y.Gu, X.Huang, V.Berry, J.Liu, Y.Teffera, L.Huang, B.Egge, E.L.Mullady, S.Schneider, P.S.Andrews, A.Mishra, J.Newcomb, R.Serafino, C.A.Strathdee, S.M.Turci, C.Wilson, E.F.Dimauro. Discovery of Novel, Induced-Pocket Binding Oxazolidinones As Potent, Selective, and Orally Bioavailable Tankyrase Inhibitors. J.Med.Chem. V. 56 4320 2013.
ISSN: ISSN 0022-2623
PubMed: 23701517
DOI: 10.1021/JM4000038
Page generated: Sun Oct 27 01:36:27 2024

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