Zinc in PDB 4k4f: Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]

Enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]

All present enzymatic activity of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide], PDB code: 4k4f was solved by X.Huang, H.Bregman, C.Wilson, E.Dimauro, H.Gunaydin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.687, 78.121, 146.644, 90.00, 90.00, 90.00
R / Rfree (%) 28 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] (pdb code 4k4f). 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 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide], PDB code: 4k4f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4k4f

Go back to Zinc Binding Sites List in 4k4f
Zinc binding site 1 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]


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 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:24.2
occ:1.00
 ND1 A:HIS1237 2.2 35.7 1.0
SG A:CYS1242 2.4 24.5 1.0
SG A:CYS1234 2.4 34.2 1.0
SG A:CYS1245 2.5 19.1 1.0
CE1 A:HIS1237 2.8 35.6 1.0
CB A:CYS1234 2.9 34.4 1.0
CB A:CYS1242 3.2 22.4 1.0
CG A:HIS1237 3.4 35.8 1.0
CB A:CYS1245 3.6 17.3 1.0
N A:HIS1237 3.9 36.5 1.0
CB A:HIS1237 4.0 35.6 1.0
NE2 A:HIS1237 4.1 35.6 1.0
N A:CYS1245 4.2 17.3 1.0
CD2 A:HIS1237 4.4 35.9 1.0
CA A:CYS1234 4.4 34.7 1.0
CA A:HIS1237 4.5 35.8 1.0
CA A:CYS1245 4.5 17.1 1.0
CA A:CYS1242 4.7 22.2 1.0
CB A:ILE1244 4.7 17.9 1.0
N A:THR1236 4.9 37.3 1.0
C A:THR1236 4.9 36.9 1.0
C A:CYS1234 4.9 35.4 1.0
CB A:THR1236 5.0 37.7 1.0

Zinc binding site 2 out of 2 in 4k4f

Go back to Zinc Binding Sites List in 4k4f
Zinc binding site 2 out of 2 in the Co-Crystal Structure of TNKS1 with Compound 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide]


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 18 [4-[(4S)-5,5-Dimethyl- 2-Oxo-4-Phenyl-1,3-Oxazolidin-3-Yl]-N-(Quinolin-8-Yl)Benzamide] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:38.0
occ:1.00
 SG B:CYS1242 2.2 31.5 1.0
ND1 B:HIS1237 2.3 37.0 1.0
SG B:CYS1234 2.5 36.3 1.0
SG B:CYS1245 2.5 26.8 1.0
CB B:CYS1234 2.7 36.5 1.0
CB B:CYS1242 3.1 29.8 1.0
CG B:HIS1237 3.2 37.0 1.0
CB B:HIS1237 3.3 37.0 1.0
CE1 B:HIS1237 3.3 37.2 1.0
CB B:CYS1245 3.7 26.0 1.0
N B:HIS1237 3.8 37.1 1.0
CA B:HIS1237 4.1 37.2 1.0
CA B:CYS1234 4.2 36.7 1.0
N B:CYS1245 4.3 25.7 1.0
CD2 B:HIS1237 4.3 37.4 1.0
NE2 B:HIS1237 4.4 37.5 1.0
CA B:CYS1242 4.5 29.7 1.0
CA B:CYS1245 4.7 25.6 1.0
CB B:THR1236 4.8 36.5 1.0
C B:THR1236 4.8 36.8 1.0
C B:HIS1237 4.8 37.1 1.0
C B:CYS1234 4.8 37.3 1.0
N B:CYS1234 4.9 37.2 1.0
CB B:ILE1244 4.9 26.1 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 01:43:00 2024

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