Fluorine in PDB 7kk3: Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib

Enzymatic activity of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib

All present enzymatic activity of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib:
2.4.2.30;

Protein crystallography data

The structure of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib, PDB code: 7kk3 was solved by K.S.Gajiwala, K.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.12 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.48, 107.68, 143.48, 90, 90, 90
R / Rfree (%) 21.3 / 25.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib (pdb code 7kk3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib, PDB code: 7kk3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7kk3

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Fluorine binding site 1 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:45.6
occ:1.00
 F2 A:2YQ9001 0.0 45.6 1.0
C14 A:2YQ9001 1.4 43.1 1.0
C15 A:2YQ9001 2.3 40.2 1.0
C13 A:2YQ9001 2.3 42.6 1.0
O A:GLY888 3.1 49.9 1.0
C A:GLY888 3.1 50.3 1.0
CA A:GLY888 3.2 50.1 1.0
C16 A:2YQ9001 3.6 41.6 1.0
C12 A:2YQ9001 3.6 41.3 1.0
N A:TYR889 3.8 45.6 1.0
C11 A:2YQ9001 4.1 39.3 1.0
N A:GLY888 4.5 50.7 1.0
O A:THR887 4.5 53.5 1.0
O A:HOH9106 4.7 41.4 1.0
CA A:TYR889 4.7 44.8 1.0
CD2 A:TYR889 4.8 49.1 1.0
CG A:GLN759 4.9 80.0 1.0
OE1 A:GLN759 4.9 92.8 1.0
C A:THR887 5.0 53.9 1.0
CE2 A:TYR889 5.0 51.0 1.0

Fluorine binding site 2 out of 8 in 7kk3

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Fluorine binding site 2 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:37.8
occ:1.00
 F1 A:2YQ9001 0.0 37.8 1.0
C9 A:2YQ9001 1.4 35.8 1.0
C10 A:2YQ9001 2.3 35.0 1.0
C8 A:2YQ9001 2.4 34.2 1.0
CE A:LYS903 3.2 47.0 1.0
CB A:GLU988 3.4 39.5 1.0
O A:PHE897 3.4 35.5 1.0
C1 A:2YQ9001 3.6 34.4 1.0
C7 A:2YQ9001 3.6 35.5 1.0
CB A:ALA898 3.7 32.1 1.0
CD A:LYS903 3.7 42.8 1.0
C A:PHE897 3.8 35.3 1.0
CG A:LYS903 3.8 38.4 1.0
CA A:ALA898 4.0 31.7 1.0
N A:ALA898 4.0 32.5 1.0
C2 A:2YQ9001 4.1 34.1 1.0
CA A:GLU988 4.2 37.9 1.0
OE2 A:GLU988 4.2 46.1 1.0
O A:ASN987 4.2 40.0 1.0
NZ A:LYS903 4.3 48.5 1.0
CD A:GLU988 4.3 51.1 1.0
CG A:GLU988 4.5 42.2 1.0
N A:PHE897 4.6 30.4 1.0
CA A:PHE897 4.6 31.0 1.0
O A:HOH9116 4.7 56.3 1.0
N3 A:2YQ9001 4.8 36.4 1.0
CB A:LYS903 4.8 35.9 1.0
OG A:SER904 4.8 43.4 1.0
OE1 A:GLU988 4.8 48.3 1.0
C4 A:2YQ9001 4.8 32.0 1.0

Fluorine binding site 3 out of 8 in 7kk3

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Fluorine binding site 3 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9001

b:69.0
occ:1.00
 F2 B:2YQ9001 0.0 69.0 1.0
C14 B:2YQ9001 1.4 66.2 1.0
C15 B:2YQ9001 2.3 64.2 1.0
C13 B:2YQ9001 2.3 64.0 1.0
O B:GLY888 2.6 52.8 1.0
C16 B:2YQ9001 3.6 61.4 1.0
C12 B:2YQ9001 3.6 61.0 1.0
C B:GLY888 3.9 53.6 1.0
C11 B:2YQ9001 4.1 57.3 1.0
O B:HOH9123 4.2 56.9 1.0
OE2 B:GLU763 4.4 88.5 1.0
CD1 B:TYR889 4.5 52.9 1.0
CA B:TYR889 4.6 49.6 1.0
N B:TYR889 4.7 50.3 1.0
CE1 B:TYR889 4.7 51.2 1.0
CD B:GLU763 4.8 97.4 1.0
OE1 B:GLN759 4.8 107.4 1.0
CA B:GLY888 4.9 48.1 1.0
CG B:TYR889 4.9 51.3 1.0

Fluorine binding site 4 out of 8 in 7kk3

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Fluorine binding site 4 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9001

b:39.7
occ:1.00
 F1 B:2YQ9001 0.0 39.7 1.0
C9 B:2YQ9001 1.4 36.6 1.0
C10 B:2YQ9001 2.3 37.0 1.0
C8 B:2YQ9001 2.3 35.1 1.0
CD B:LYS903 3.3 65.3 1.0
O B:PHE897 3.5 37.6 1.0
C1 B:2YQ9001 3.6 36.5 1.0
C7 B:2YQ9001 3.6 36.2 1.0
CE B:LYS903 3.6 71.8 1.0
CB B:ALA898 3.6 38.6 1.0
C B:PHE897 3.8 39.6 1.0
CG B:GLU988 3.9 58.2 1.0
O B:ASN987 3.9 51.0 1.0
CG B:LYS903 4.0 61.1 1.0
CA B:ALA898 4.1 38.4 1.0
N B:ALA898 4.1 38.6 1.0
C2 B:2YQ9001 4.1 35.8 1.0
CD B:GLU988 4.1 72.5 1.0
CA B:GLU988 4.2 44.5 1.0
OE2 B:GLU988 4.2 62.4 1.0
NZ B:LYS903 4.2 68.7 1.0
CB B:GLU988 4.2 45.7 1.0
N B:PHE897 4.6 37.5 1.0
CB B:LYS903 4.6 47.1 1.0
CA B:PHE897 4.7 37.9 1.0
N3 B:2YQ9001 4.8 40.0 1.0
OE1 B:GLU988 4.8 59.9 1.0
C B:ASN987 4.8 52.3 1.0
C4 B:2YQ9001 4.8 36.9 1.0
N B:GLU988 4.9 46.3 1.0
CB B:TYR896 5.0 38.2 1.0
CE2 B:TYR907 5.0 41.3 1.0

Fluorine binding site 5 out of 8 in 7kk3

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Fluorine binding site 5 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:57.2
occ:1.00
 F2 C:2YQ9001 0.0 57.2 1.0
C14 C:2YQ9001 1.4 54.9 1.0
C15 C:2YQ9001 2.3 51.0 1.0
C13 C:2YQ9001 2.3 55.2 1.0
O C:GLY888 2.9 49.6 1.0
O C:HOH9188 2.9 47.9 1.0
NE2 C:GLN759 3.3 64.6 1.0
C16 C:2YQ9001 3.6 51.2 1.0
C12 C:2YQ9001 3.6 52.2 1.0
CD C:GLN759 3.8 74.2 1.0
C C:GLY888 3.9 46.5 1.0
CG C:GLN759 3.9 53.9 1.0
OE2 C:GLU763 3.9 73.3 1.0
C11 C:2YQ9001 4.1 48.5 1.0
CD C:GLU763 4.3 77.7 1.0
O C:HOH9134 4.4 39.0 1.0
CG C:GLU763 4.5 55.5 1.0
O C:HOH9114 4.6 53.2 1.0
CA C:GLY888 4.6 38.7 1.0
CD2 C:TYR889 4.7 37.2 1.0
N C:TYR889 4.7 42.0 1.0
CE2 C:TYR889 4.8 37.7 1.0
OE1 C:GLN759 4.8 71.7 1.0
CA C:TYR889 4.8 40.2 1.0

Fluorine binding site 6 out of 8 in 7kk3

Go back to Fluorine Binding Sites List in 7kk3
Fluorine binding site 6 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F9001

b:35.8
occ:1.00
 F1 C:2YQ9001 0.0 35.8 1.0
C9 C:2YQ9001 1.4 34.5 1.0
C10 C:2YQ9001 2.3 33.9 1.0
C8 C:2YQ9001 2.4 34.2 1.0
CD C:LYS903 3.3 50.5 1.0
CG C:GLU988 3.3 47.7 1.0
O C:PHE897 3.4 33.3 1.0
C1 C:2YQ9001 3.6 32.9 1.0
C7 C:2YQ9001 3.6 35.3 1.0
CB C:ALA898 3.7 33.6 1.0
C C:PHE897 3.7 35.0 1.0
CG C:LYS903 3.7 40.6 1.0
CE C:LYS903 3.9 69.3 1.0
N C:ALA898 4.0 33.9 1.0
CA C:ALA898 4.0 33.3 1.0
O C:ASN987 4.0 41.9 1.0
CD C:GLU988 4.1 62.4 1.0
C2 C:2YQ9001 4.1 31.5 1.0
CA C:GLU988 4.1 37.0 1.0
CB C:GLU988 4.2 37.7 1.0
OE2 C:GLU988 4.4 59.7 1.0
N C:PHE897 4.5 31.2 1.0
CA C:PHE897 4.5 30.0 1.0
CB C:LYS903 4.6 41.9 1.0
NZ C:LYS903 4.6 69.2 1.0
OE1 C:GLU988 4.7 57.1 1.0
N3 C:2YQ9001 4.8 37.6 1.0
C4 C:2YQ9001 4.8 33.7 1.0
CE2 C:TYR907 4.9 35.0 1.0
C C:ASN987 4.9 44.6 1.0
CB C:TYR896 5.0 31.5 1.0
N C:GLU988 5.0 38.9 1.0

Fluorine binding site 7 out of 8 in 7kk3

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Fluorine binding site 7 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F9001

b:61.9
occ:1.00
 F2 D:2YQ9001 0.0 61.9 1.0
C14 D:2YQ9001 1.4 56.9 1.0
C15 D:2YQ9001 2.3 51.5 1.0
C13 D:2YQ9001 2.3 54.7 1.0
O D:GLY888 3.0 56.5 1.0
C D:GLY888 3.0 57.3 1.0
CD D:GLN759 3.1 129.4 1.0
OE1 D:GLN759 3.1 123.2 1.0
CA D:GLY888 3.2 54.3 1.0
NE2 D:GLN759 3.2 117.3 1.0
C16 D:2YQ9001 3.6 50.7 1.0
C12 D:2YQ9001 3.6 49.6 1.0
CG D:GLN759 3.8 115.7 1.0
N D:TYR889 3.8 53.2 1.0
C11 D:2YQ9001 4.1 49.3 1.0
O D:THR887 4.5 58.7 1.0
N D:GLY888 4.5 55.2 1.0
CA D:TYR889 4.5 53.2 1.0
O D:HOH9105 4.7 46.2 1.0
CD2 D:TYR889 4.8 59.0 1.0
CG D:TYR889 4.9 57.8 1.0
C D:THR887 4.9 59.7 1.0
CE2 D:TYR889 4.9 60.2 1.0

Fluorine binding site 8 out of 8 in 7kk3

Go back to Fluorine Binding Sites List in 7kk3
Fluorine binding site 8 out of 8 in the Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the Catalytic Domain of PARP1 in Complex with Talazoparib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F9001

b:44.9
occ:1.00
 F1 D:2YQ9001 0.0 44.9 1.0
C9 D:2YQ9001 1.4 43.9 1.0
C10 D:2YQ9001 2.3 44.6 1.0
C8 D:2YQ9001 2.3 45.5 1.0
O D:PHE897 3.2 42.6 1.0
CB D:GLU988 3.4 46.0 1.0
C D:PHE897 3.5 42.9 1.0
CE D:LYS903 3.5 59.1 1.0
C1 D:2YQ9001 3.6 45.0 1.0
C7 D:2YQ9001 3.6 45.3 1.0
CD D:LYS903 3.7 51.1 1.0
CB D:ALA898 3.7 41.5 1.0
N D:ALA898 3.8 41.5 1.0
CA D:ALA898 3.9 41.4 1.0
CG D:LYS903 4.0 47.3 1.0
C2 D:2YQ9001 4.1 44.8 1.0
CA D:GLU988 4.1 44.6 1.0
NZ D:LYS903 4.2 62.0 1.0
O D:ASN987 4.2 48.7 1.0
OE2 D:GLU988 4.4 52.8 1.0
N D:PHE897 4.4 38.1 1.0
CA D:PHE897 4.4 37.1 1.0
CD D:GLU988 4.5 68.2 1.0
CG D:GLU988 4.5 52.9 1.0
CB D:LYS903 4.7 49.1 1.0
N3 D:2YQ9001 4.7 44.8 1.0
C4 D:2YQ9001 4.8 44.7 1.0
C D:TYR896 4.9 41.0 1.0
OE1 D:GLU988 5.0 58.5 1.0
CB D:TYR896 5.0 39.5 1.0
OG D:SER904 5.0 56.4 1.0

Reference:

K.Ryan, B.Bolanos, M.Smith, P.Palde, P.D.Cuenca, T.L.Vanarsdale, S.Niessen, L.Zhang, D.Behenna, M.A.Ornelas, K.T.Tran, S.Kaiser, L.Lum, A.Stewart, K.S.Gajiwala. Dissecting the Molecular Determinants of Clinical PARP1 Inhibitor Selectivity For TANKYRASE1. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33361107
DOI: 10.1074/JBC.RA120.016573
Page generated: Fri Aug 2 08:21:33 2024

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