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Fluorine in PDB 5kpp: Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor

Enzymatic activity of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor

All present enzymatic activity of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor:
2.4.2.30;

Protein crystallography data

The structure of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor, PDB code: 5kpp was solved by R.Cao, Y.L.Wang, J.Zhou, N.Huang, B.L.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.74 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.656, 92.691, 163.487, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor (pdb code 5kpp). 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 Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor, PDB code: 5kpp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5kpp

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Fluorine binding site 1 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:28.8
occ:1.00
 FAE A:6WZ1101 0.0 28.8 1.0
CAX A:6WZ1101 1.4 28.3 1.0
CAL A:6WZ1101 2.4 27.3 1.0
CAY A:6WZ1101 2.4 28.6 1.0
CAV A:6WZ1101 2.8 29.6 1.0
CAP A:6WZ1101 3.1 29.7 1.0
NBE A:6WZ1101 3.1 29.3 1.0
CE1 A:TYR896 3.2 26.6 1.0
CD1 A:TYR896 3.3 26.4 1.0
O A:GLY894 3.3 32.4 1.0
CD2 A:TYR889 3.4 35.7 1.0
OAB A:6WZ1101 3.7 28.9 1.0
CAK A:6WZ1101 3.7 27.1 1.0
CAO A:6WZ1101 3.7 28.0 1.0
CE2 A:TYR889 4.0 35.9 1.0
CZ A:TYR896 4.0 26.8 1.0
CG A:TYR896 4.2 26.8 1.0
CAW A:6WZ1101 4.2 27.6 1.0
CAS A:6WZ1101 4.3 29.7 1.0
C A:GLY894 4.3 31.9 1.0
CG A:TYR889 4.4 35.9 1.0
N A:GLY894 4.5 34.8 1.0
CB A:TYR889 4.6 35.7 1.0
CAQ A:6WZ1101 4.6 29.4 1.0
OH A:TYR896 4.6 25.7 1.0
O A:GLY892 4.7 35.3 1.0
CE2 A:TYR896 4.8 26.5 1.0
CD2 A:TYR896 4.8 26.6 1.0
CB A:TYR896 4.9 26.9 1.0

Fluorine binding site 2 out of 8 in 5kpp

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Fluorine binding site 2 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:31.3
occ:1.00
 FAG A:6WZ1101 0.0 31.3 1.0
CBH A:6WZ1101 1.3 30.6 1.0
FAH A:6WZ1101 2.1 31.2 1.0
FAF A:6WZ1101 2.2 30.2 1.0
CAT A:6WZ1101 2.3 30.2 1.0
NBF A:6WZ1101 2.9 29.7 1.0
O A:HOH1233 3.5 39.9 1.0
CBD A:6WZ1101 3.7 29.6 1.0
CB A:ARG878 3.8 33.0 1.0
OD2 A:ASP770 4.0 34.9 1.0
NE A:ARG878 4.0 33.9 1.0
CAQ A:6WZ1101 4.2 29.4 1.0
NH2 A:ARG878 4.2 33.9 1.0
OD1 A:ASP770 4.2 37.0 1.0
O A:ARG878 4.3 34.3 1.0
CZ A:ARG878 4.3 34.2 1.0
CG A:ASP770 4.4 36.4 1.0
C A:ARG878 4.4 33.8 1.0
CD1 A:LEU769 4.4 39.7 1.0
CA A:ARG878 4.6 32.8 1.0
CAA A:6WZ1101 4.6 29.5 1.0
O A:ASP766 4.6 32.1 1.0
O A:ILE879 4.7 37.0 1.0
N A:ARG878 4.7 31.6 1.0
CG A:ARG878 4.8 33.1 1.0
CD A:ARG878 4.8 33.9 1.0
CAS A:6WZ1101 4.8 29.7 1.0
CB A:LEU769 4.9 37.2 1.0
C A:ILE879 4.9 36.7 1.0

Fluorine binding site 3 out of 8 in 5kpp

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Fluorine binding site 3 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:31.2
occ:1.00
 FAH A:6WZ1101 0.0 31.2 1.0
CBH A:6WZ1101 1.3 30.6 1.0
FAF A:6WZ1101 2.1 30.2 1.0
FAG A:6WZ1101 2.1 31.3 1.0
CAT A:6WZ1101 2.3 30.2 1.0
O A:ILE879 3.3 37.0 1.0
CD1 A:LEU769 3.4 39.7 1.0
CA A:ALA880 3.5 37.6 1.0
C A:ILE879 3.6 36.7 1.0
NBF A:6WZ1101 3.6 29.7 1.0
N A:ALA880 3.7 36.6 1.0
CD A:PRO881 4.1 40.0 1.0
CB A:ALA880 4.3 36.5 1.0
O A:HOH1283 4.3 47.2 1.0
CB A:ARG878 4.5 33.0 1.0
CAQ A:6WZ1101 4.5 29.4 1.0
C A:ALA880 4.5 38.8 1.0
N A:PRO881 4.6 39.9 1.0
CBD A:6WZ1101 4.7 29.6 1.0
C A:ARG878 4.7 33.8 1.0
N A:ILE879 4.7 34.8 1.0
CA A:ILE879 4.7 35.8 1.0
O A:ARG878 4.7 34.3 1.0
CG A:LEU769 4.7 38.8 1.0
OH A:TYR710 4.8 34.9 1.0
OD1 A:ASP766 4.8 33.5 1.0
CB A:LEU769 4.9 37.2 1.0
O A:HOH1233 4.9 39.9 1.0

Fluorine binding site 4 out of 8 in 5kpp

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Fluorine binding site 4 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:30.2
occ:1.00
 FAF A:6WZ1101 0.0 30.2 1.0
CBH A:6WZ1101 1.3 30.6 1.0
FAH A:6WZ1101 2.1 31.2 1.0
FAG A:6WZ1101 2.2 31.3 1.0
CAT A:6WZ1101 2.3 30.2 1.0
NBF A:6WZ1101 2.9 29.7 1.0
O A:HOH1233 3.1 39.9 1.0
O A:ASP766 3.3 32.1 1.0
CAQ A:6WZ1101 3.4 29.4 1.0
CA A:ASP766 3.4 32.3 1.0
CB A:ASP766 3.5 32.8 1.0
C A:ASP766 3.7 32.4 1.0
OD1 A:ASP766 3.8 33.5 1.0
CD1 A:LEU769 3.9 39.7 1.0
CG A:ASP766 3.9 33.9 1.0
CBD A:6WZ1101 4.2 29.6 1.0
CB A:LEU769 4.3 37.2 1.0
OH A:TYR710 4.3 34.9 1.0
CAP A:6WZ1101 4.6 29.7 1.0
CG A:LEU769 4.7 38.8 1.0
N A:ASP766 4.7 31.6 1.0
OD2 A:ASP766 4.8 34.5 1.0
OD2 A:ASP770 4.8 34.9 1.0
CA A:ALA880 4.9 37.6 1.0

Fluorine binding site 5 out of 8 in 5kpp

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Fluorine binding site 5 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:35.3
occ:1.00
 FAE B:6WZ1101 0.0 35.3 1.0
CAX B:6WZ1101 1.3 36.6 1.0
CAL B:6WZ1101 2.4 37.3 1.0
CAY B:6WZ1101 2.4 36.7 1.0
CAV B:6WZ1101 2.8 38.1 1.0
CE1 B:TYR896 3.0 33.7 1.0
CAP B:6WZ1101 3.0 40.4 1.0
NBE B:6WZ1101 3.1 39.5 1.0
CD1 B:TYR896 3.1 34.0 1.0
CD2 B:TYR889 3.4 38.5 1.0
CAK B:6WZ1101 3.6 37.4 1.0
CAO B:6WZ1101 3.6 37.0 1.0
O B:GLY894 3.7 36.3 1.0
OAB B:6WZ1101 3.7 36.9 1.0
CZ B:TYR896 3.8 33.3 1.0
CE2 B:TYR889 4.0 38.0 1.0
CG B:TYR896 4.0 34.5 1.0
CAW B:6WZ1101 4.2 37.9 1.0
CG B:TYR889 4.2 38.8 1.0
CAS B:6WZ1101 4.3 40.8 1.0
OH B:TYR896 4.4 34.0 1.0
CB B:TYR889 4.4 39.6 1.0
CE2 B:TYR896 4.5 34.5 1.0
CAQ B:6WZ1101 4.5 41.5 1.0
C B:GLY894 4.6 35.9 1.0
O B:GLY892 4.6 36.1 1.0
CD2 B:TYR896 4.6 34.4 1.0
N B:GLY894 4.7 35.7 1.0
O B:HOH1235 4.7 54.1 1.0
CB B:TYR896 4.8 35.7 1.0

Fluorine binding site 6 out of 8 in 5kpp

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Fluorine binding site 6 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:46.1
occ:1.00
 FAG B:6WZ1101 0.0 46.1 1.0
CBH B:6WZ1101 1.4 46.2 1.0
FAH B:6WZ1101 2.2 48.6 1.0
FAF B:6WZ1101 2.2 46.4 1.0
CAT B:6WZ1101 2.4 44.7 1.0
NBF B:6WZ1101 2.8 42.5 1.0
CAQ B:6WZ1101 3.1 41.5 1.0
CB B:ASP766 3.2 36.8 1.0
CA B:ASP766 3.2 37.5 1.0
O B:ASP766 3.3 37.3 1.0
OD1 B:ASP766 3.4 36.6 1.0
CG B:ASP766 3.6 37.3 1.0
C B:ASP766 3.6 38.2 1.0
CD1 B:LEU769 4.0 44.5 1.0
CBD B:6WZ1101 4.2 41.5 1.0
OH B:TYR710 4.2 34.7 1.0
OD2 B:ASP770 4.3 45.4 1.0
CB B:LEU769 4.4 42.4 1.0
CAP B:6WZ1101 4.5 40.4 1.0
N B:ASP766 4.6 37.3 1.0
OD2 B:ASP766 4.6 37.7 1.0
CG B:LEU769 4.8 43.9 1.0
N B:ASN767 4.9 39.6 1.0

Fluorine binding site 7 out of 8 in 5kpp

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Fluorine binding site 7 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:48.6
occ:1.00
 FAH B:6WZ1101 0.0 48.6 1.0
CBH B:6WZ1101 1.3 46.2 1.0
FAF B:6WZ1101 2.2 46.4 1.0
FAG B:6WZ1101 2.2 46.1 1.0
CAT B:6WZ1101 2.3 44.7 1.0
NBF B:6WZ1101 3.0 42.5 1.0
O B:HOH1224 3.4 41.0 1.0
OD2 B:ASP770 3.5 45.4 1.0
CBD B:6WZ1101 3.8 41.5 1.0
NH2 B:ARG878 4.1 54.3 1.0
CG B:ASP770 4.1 46.5 1.0
CAQ B:6WZ1101 4.1 41.5 1.0
OD1 B:ASP770 4.2 50.4 1.0
NE B:ARG878 4.3 53.1 1.0
O B:ASP766 4.3 37.3 1.0
CD1 B:LEU769 4.4 44.5 1.0
CB B:ARG878 4.4 46.3 1.0
CZ B:ARG878 4.5 53.7 1.0
O B:ARG878 4.6 45.6 1.0
CAA B:6WZ1101 4.6 41.4 1.0
CB B:LEU769 4.7 42.4 1.0
C B:ARG878 4.9 44.3 1.0
CAS B:6WZ1101 5.0 40.8 1.0

Fluorine binding site 8 out of 8 in 5kpp

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Fluorine binding site 8 out of 8 in the Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2, 4(1H,3H)-Dione Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:46.4
occ:1.00
 FAF B:6WZ1101 0.0 46.4 1.0
CBH B:6WZ1101 1.4 46.2 1.0
FAH B:6WZ1101 2.2 48.6 1.0
FAG B:6WZ1101 2.2 46.1 1.0
CAT B:6WZ1101 2.4 44.7 1.0
CD1 B:LEU769 3.2 44.5 1.0
CA B:ALA880 3.7 38.1 1.0
NBF B:6WZ1101 3.7 42.5 1.0
O B:ILE879 3.8 40.4 1.0
N B:ALA880 3.9 38.8 1.0
CD B:PRO881 3.9 38.5 1.0
C B:ILE879 4.0 41.0 1.0
CAQ B:6WZ1101 4.4 41.5 1.0
CG B:LEU769 4.5 43.9 1.0
CB B:ALA880 4.6 37.5 1.0
OD1 B:ASP766 4.6 36.6 1.0
O B:HOH1217 4.6 47.8 1.0
C B:ALA880 4.6 37.6 1.0
N B:PRO881 4.6 38.1 1.0
CB B:LEU769 4.6 42.4 1.0
OH B:TYR710 4.7 34.7 1.0
NH2 B:ARG878 4.8 54.3 1.0
CBD B:6WZ1101 4.8 41.5 1.0
CB B:ARG878 4.8 46.3 1.0
CZ B:ARG878 4.9 53.7 1.0
O B:ARG878 4.9 45.6 1.0
C B:ARG878 5.0 44.3 1.0

Reference:

R.Cao, Y.L.Wang, J.Zhou, N.Huang, B.L.Xu. Structure of Human PARP1 Catalytic Domain Bound to A Quinazoline-2,4(1H,3H)-Dione Inhibitor To Be Published.
Page generated: Thu Aug 1 11:13:16 2024

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