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Fluorine in PDB 4li8: Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide

Enzymatic activity of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide

All present enzymatic activity of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide:
2.4.2.30;

Protein crystallography data

The structure of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide, PDB code: 4li8 was solved by C.A.Kirby, T.Stams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.04 / 2.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.700, 43.100, 88.100, 90.00, 91.30, 90.00
R / Rfree (%) 20.7 / 28.3

Other elements in 4li8:

The structure of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide (pdb code 4li8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide, PDB code: 4li8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4li8

Go back to Fluorine Binding Sites List in 4li8
Fluorine binding site 1 out of 2 in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1402

b:43.6
occ:1.00
 F1 A:1XQ1402 0.0 43.6 1.0
C19 A:1XQ1402 1.4 39.2 1.0
C20 A:1XQ1402 2.4 26.6 1.0
C21 A:1XQ1402 2.4 31.5 1.0
CB A:ALA1191 3.2 31.9 1.0
C22 A:1XQ1402 3.7 27.3 1.0
C18 A:1XQ1402 3.7 29.8 1.0
NE2 A:HIS1201 4.0 38.6 1.0
CE1 A:HIS1201 4.0 37.0 1.0
C17 A:1XQ1402 4.2 28.0 1.0
ND1 A:HIS1201 4.5 36.5 1.0
CD2 A:HIS1201 4.5 36.7 1.0
CA A:ALA1191 4.6 37.4 1.0
CB A:PHE1188 4.8 28.3 1.0
CG A:HIS1201 4.8 35.8 1.0
CD1 A:PHE1188 4.8 27.3 1.0

Fluorine binding site 2 out of 2 in 4li8

Go back to Fluorine Binding Sites List in 4li8
Fluorine binding site 2 out of 2 in the Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tankyrase-1 Complexed with Small Molecule Inhibitor 2-[4-(4- Fluorobenzoyl)Piperidin-1-Yl]-N-[(4-Oxo-3,5,7,8-Tetrahydro-4H- Pyrano[4,3-D]Pyrimidin-2-Yl)Methyl]-N-(Thiophen-2-Ylmethyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1402

b:43.8
occ:1.00
 F1 B:1XQ1402 0.0 43.8 1.0
C19 B:1XQ1402 1.4 37.9 1.0
C21 B:1XQ1402 2.4 33.0 1.0
C20 B:1XQ1402 2.4 34.3 1.0
CB B:ALA1191 3.4 35.4 1.0
NE2 B:HIS1201 3.5 34.8 1.0
C18 B:1XQ1402 3.7 34.0 1.0
C22 B:1XQ1402 3.7 31.6 1.0
CE1 B:HIS1201 3.7 43.3 1.0
CD2 B:HIS1201 4.1 39.0 1.0
C17 B:1XQ1402 4.2 32.8 1.0
ND1 B:HIS1201 4.3 42.3 1.0
CG B:HIS1201 4.5 41.4 1.0
CB B:PHE1188 4.5 32.6 1.0
CA B:ALA1191 4.8 36.5 1.0
CG B:PHE1188 4.9 33.0 1.0
CD1 B:PHE1188 5.0 37.5 1.0

Reference:

M.D.Shultz, A.K.Cheung, C.A.Kirby, B.Firestone, J.Fan, C.H.Chen, Z.Chen, D.N.Chin, L.Dipietro, A.Fazal, Y.Feng, P.D.Fortin, T.Gould, B.Lagu, H.Lei, F.Lenoir, D.Majumdar, E.Ochala, M.G.Palermo, L.Pham, M.Pu, T.Smith, T.Stams, R.C.Tomlinson, B.B.Toure, M.Visser, R.M.Wang, N.J.Waters, W.Shao. Identification of Nvp-TNKS656: the Use of Structure-Efficiency Relationships to Generate A Highly Potent, Selective, and Orally Active Tankyrase Inhibitor. J.Med.Chem. V. 56 6495 2013.
ISSN: ISSN 0022-2623
PubMed: 23844574
DOI: 10.1021/JM400807N
Page generated: Mon Jul 14 23:02:50 2025

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