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Zinc in PDB 4n4v: Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One]

Enzymatic activity of Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One]

All present enzymatic activity of Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One]:
2.4.2.30;

Protein crystallography data

The structure of Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One], PDB code: 4n4v was solved by X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.986, 77.715, 147.777, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One] (pdb code 4n4v). 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 Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One], PDB code: 4n4v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4n4v

Go back to Zinc Binding Sites List in 4n4v
Zinc binding site 1 out of 2 in the Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One]


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 Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:26.5
occ:1.00
 ND1 A:HIS1237 2.2 30.6 1.0
SG A:CYS1242 2.3 23.4 1.0
SG A:CYS1234 2.4 28.8 1.0
SG A:CYS1245 2.4 23.0 1.0
CE1 A:HIS1237 3.0 30.4 1.0
CG A:HIS1237 3.2 30.9 1.0
CB A:CYS1234 3.3 28.7 1.0
CB A:CYS1242 3.3 23.0 1.0
CB A:CYS1245 3.3 22.4 1.0
CB A:HIS1237 3.7 30.3 1.0
N A:HIS1237 3.8 30.4 1.0
N A:CYS1245 3.9 22.2 1.0
NE2 A:HIS1237 4.0 30.7 1.0
CD2 A:HIS1237 4.2 30.9 1.0
CA A:CYS1245 4.2 22.2 1.0
CA A:HIS1237 4.4 30.2 1.0
CB A:THR1236 4.5 30.9 1.0
CB A:ILE1244 4.5 22.8 1.0
O A:HOH1627 4.5 32.2 1.0
O A:HOH1639 4.5 38.2 1.0
CA A:CYS1234 4.7 28.7 1.0
CA A:CYS1242 4.7 23.1 1.0
C A:THR1236 4.8 30.8 1.0
N A:THR1236 4.8 30.4 1.0
CG2 A:ILE1244 4.9 23.2 1.0
CA A:THR1236 4.9 30.6 1.0
C A:ILE1244 5.0 22.4 1.0

Zinc binding site 2 out of 2 in 4n4v

Go back to Zinc Binding Sites List in 4n4v
Zinc binding site 2 out of 2 in the Co-Crystal Structure of Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One]


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 Tankyrase 1 with Compound 4 [(4S)-3-{Trans-4- [6-Amino-5-(Pyrimidin-2-Yl)Pyridin-3-Yl]Cyclohexyl}-5,5-Dimethyl-4- Phenyl-1,3-Oxazolidin-2-One] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1401

b:29.7
occ:1.00
 ND1 B:HIS1237 2.2 32.6 1.0
SG B:CYS1242 2.4 26.8 1.0
SG B:CYS1245 2.4 25.6 1.0
SG B:CYS1234 2.4 31.6 1.0
CG B:HIS1237 3.0 32.8 1.0
CE1 B:HIS1237 3.1 32.8 1.0
CB B:CYS1245 3.2 25.4 1.0
CB B:HIS1237 3.3 32.7 1.0
CB B:CYS1234 3.3 32.0 1.0
CB B:CYS1242 3.4 27.0 1.0
N B:HIS1237 3.8 32.7 1.0
N B:CYS1245 3.9 25.8 1.0
CD2 B:HIS1237 4.0 32.9 1.0
NE2 B:HIS1237 4.1 32.9 1.0
CA B:HIS1237 4.2 32.5 1.0
CA B:CYS1245 4.2 25.7 1.0
O B:HOH1533 4.2 30.5 1.0
O B:HOH1519 4.3 30.9 1.0
CB B:ILE1244 4.7 26.1 1.0
CA B:CYS1234 4.7 31.9 1.0
CB B:THR1236 4.7 32.2 1.0
CA B:CYS1242 4.8 26.9 1.0
C B:THR1236 4.8 32.7 1.0
C B:HIS1237 5.0 32.2 1.0

Reference:

H.Huang, A.Guzman-Perez, L.Acquaviva, V.Berry, H.Bregman, J.Dovey, H.Gunaydin, X.Huang, L.Huang, D.Saffran, R.Serafino, S.Schneider, C.Wilson, E.F.Dimauro. Structure-Based Design of 2-Aminopyridine Oxazolidinones As Potent and Selective Tankyrase Inhibitors. Acs Med Chem Lett V. 4 1218 2013.
ISSN: ISSN 1948-5875
PubMed: 24900633
DOI: 10.1021/ML4003315
Page generated: Sun Oct 27 03:00:54 2024

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