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Fluorine in PDB 4r5w: Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939

Enzymatic activity of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939

All present enzymatic activity of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939:
2.4.2.30;

Protein crystallography data

The structure of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939, PDB code: 4r5w was solved by T.Karlberg, A.G.Thorsell, H.Schuler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.46 / 2.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.525, 67.662, 91.165, 90.00, 111.28, 90.00
R / Rfree (%) 19.2 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 (pdb code 4r5w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939, PDB code: 4r5w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4r5w

Go back to Fluorine Binding Sites List in 4r5w
Fluorine binding site 1 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:65.2
occ:1.00
 FAB A:XAV1106 0.0 65.2 1.0
CAU A:XAV1106 1.4 63.3 1.0
FAD A:XAV1106 2.2 65.4 1.0
FAC A:XAV1106 2.3 60.0 1.0
CAQ A:XAV1106 2.3 59.5 1.0
CAH A:XAV1106 2.9 58.9 1.0
OD2 A:ASP766 3.0 46.1 1.0
CB A:ASP766 3.1 28.1 1.0
CAG A:XAV1106 3.4 56.4 1.0
CG A:ASP766 3.5 39.2 1.0
CAF A:XAV1106 4.2 57.0 1.0
O A:GLU763 4.2 36.3 1.0
ND2 A:ASN767 4.3 36.4 1.0
O2 A:SO41105 4.4 93.7 1.0
CA A:ASP766 4.5 26.3 1.0
OD1 A:ASN767 4.5 39.5 1.0
OE2 A:GLU763 4.5 79.3 1.0
CAE A:XAV1106 4.5 54.6 1.0
CG A:ASN767 4.6 39.3 1.0
C A:ASP766 4.6 28.2 1.0
N A:ASN767 4.7 26.5 1.0
OD1 A:ASP766 4.8 40.0 1.0
CAP A:XAV1106 4.8 53.8 1.0
CA A:GLU763 4.9 31.2 1.0
CG A:GLU763 4.9 54.9 1.0

Fluorine binding site 2 out of 6 in 4r5w

Go back to Fluorine Binding Sites List in 4r5w
Fluorine binding site 2 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:60.0
occ:1.00
 FAC A:XAV1106 0.0 60.0 1.0
CAU A:XAV1106 1.4 63.3 1.0
FAB A:XAV1106 2.3 65.2 1.0
FAD A:XAV1106 2.4 65.4 1.0
CAQ A:XAV1106 2.4 59.5 1.0
CAH A:XAV1106 2.9 58.9 1.0
CAG A:XAV1106 3.5 56.4 1.0
CB A:ASP766 3.9 28.1 1.0
CAF A:XAV1106 4.2 57.0 1.0
OD2 A:ASP766 4.3 46.1 1.0
OD2 A:ASP770 4.3 59.7 1.0
ND2 A:ASN868 4.4 39.6 1.0
CG A:ASP766 4.5 39.2 1.0
O A:ASP766 4.5 26.1 1.0
C A:ASP766 4.5 28.2 1.0
OG A:SER864 4.6 36.9 1.0
CAE A:XAV1106 4.7 54.6 1.0
OD1 A:ASN767 4.7 39.5 1.0
O1 A:SO41105 4.7 90.3 1.0
CA A:ASP766 4.8 26.3 1.0
N A:ASN767 4.9 26.5 1.0
O3 A:SO41105 4.9 93.9 1.0
CAP A:XAV1106 4.9 53.8 1.0

Fluorine binding site 3 out of 6 in 4r5w

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Fluorine binding site 3 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:65.4
occ:1.00
 FAD A:XAV1106 0.0 65.4 1.0
CAU A:XAV1106 1.4 63.3 1.0
FAB A:XAV1106 2.2 65.2 1.0
CAQ A:XAV1106 2.3 59.5 1.0
FAC A:XAV1106 2.4 60.0 1.0
CAG A:XAV1106 2.6 56.4 1.0
OD1 A:ASN767 2.7 39.5 1.0
ND2 A:ASN868 3.3 39.6 1.0
CG A:ASN767 3.3 39.3 1.0
ND2 A:ASN767 3.5 36.4 1.0
CAH A:XAV1106 3.6 58.9 1.0
CAE A:XAV1106 4.0 54.6 1.0
OG A:SER864 4.1 36.9 1.0
CB A:ASP766 4.4 28.1 1.0
CG A:ASN868 4.4 47.7 1.0
N A:ASN767 4.4 26.5 1.0
CB A:ASN767 4.5 27.6 1.0
CA A:ASN767 4.5 26.8 1.0
OE2 A:GLU763 4.5 79.3 1.0
C A:ASP766 4.7 28.2 1.0
CAF A:XAV1106 4.7 57.0 1.0
O A:GLU763 4.8 36.3 1.0
OD1 A:ASN868 4.8 42.2 1.0
CAP A:XAV1106 4.9 53.8 1.0
O A:ASP766 5.0 26.1 1.0

Fluorine binding site 4 out of 6 in 4r5w

Go back to Fluorine Binding Sites List in 4r5w
Fluorine binding site 4 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1103

b:71.6
occ:1.00
 FAB B:XAV1103 0.0 71.6 1.0
CAU B:XAV1103 1.3 72.6 1.0
FAD B:XAV1103 2.1 76.0 1.0
CAQ B:XAV1103 2.3 67.9 1.0
FAC B:XAV1103 2.3 73.1 1.0
CAH B:XAV1103 2.7 65.3 1.0
CB B:ASP766 3.0 32.0 1.0
OD2 B:ASP766 3.1 49.3 1.0
CAG B:XAV1103 3.4 64.7 1.0
CG B:ASP766 3.5 43.1 1.0
CAF B:XAV1103 4.0 63.0 1.0
ND2 B:ASN767 4.1 34.4 1.0
O B:GLU763 4.1 39.8 1.0
OD1 B:ASN767 4.3 45.7 1.0
CA B:ASP766 4.3 28.9 1.0
CG B:ASN767 4.3 42.7 1.0
C B:ASP766 4.4 27.7 1.0
N B:ASN767 4.4 23.1 1.0
CAE B:XAV1103 4.5 61.0 1.0
OD1 B:ASP766 4.8 43.0 1.0
CAP B:XAV1103 4.8 58.4 1.0
CA B:GLU763 4.9 34.5 1.0
CG B:GLU763 4.9 58.2 1.0
O B:ASP766 4.9 26.4 1.0
C B:GLU763 4.9 38.6 1.0

Fluorine binding site 5 out of 6 in 4r5w

Go back to Fluorine Binding Sites List in 4r5w
Fluorine binding site 5 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1103

b:73.1
occ:1.00
 FAC B:XAV1103 0.0 73.1 1.0
CAU B:XAV1103 1.4 72.6 1.0
FAD B:XAV1103 2.2 76.0 1.0
FAB B:XAV1103 2.3 71.6 1.0
CAQ B:XAV1103 2.4 67.9 1.0
CAH B:XAV1103 3.0 65.3 1.0
CAG B:XAV1103 3.4 64.7 1.0
O B:HOH1201 3.5 12.9 1.0
CB B:ASP766 3.8 32.0 1.0
O B:HOH1202 4.1 24.9 1.0
OD2 B:ASP766 4.2 49.3 1.0
OD2 B:ASP770 4.2 60.7 1.0
O B:ASP766 4.3 26.4 1.0
CAF B:XAV1103 4.3 63.0 1.0
C B:ASP766 4.4 27.7 1.0
CG B:ASP766 4.4 43.1 1.0
ND2 B:ASN868 4.4 26.7 1.0
CAE B:XAV1103 4.6 61.0 1.0
CA B:ASP766 4.6 28.9 1.0
OD1 B:ASN767 4.7 45.7 1.0
OG B:SER864 4.7 37.5 1.0
N B:ASN767 4.8 23.1 1.0
CAP B:XAV1103 5.0 58.4 1.0

Fluorine binding site 6 out of 6 in 4r5w

Go back to Fluorine Binding Sites List in 4r5w
Fluorine binding site 6 out of 6 in the Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human ARTD1 (PARP1) - Catalytic Domain in Complex with Inhibitor XAV939 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1103

b:76.0
occ:1.00
 FAD B:XAV1103 0.0 76.0 1.0
CAU B:XAV1103 1.3 72.6 1.0
FAB B:XAV1103 2.1 71.6 1.0
FAC B:XAV1103 2.2 73.1 1.0
CAQ B:XAV1103 2.4 67.9 1.0
OD1 B:ASN767 2.7 45.7 1.0
CAG B:XAV1103 2.8 64.7 1.0
ND2 B:ASN868 3.1 26.7 1.0
CG B:ASN767 3.3 42.7 1.0
ND2 B:ASN767 3.6 34.4 1.0
CAH B:XAV1103 3.6 65.3 1.0
OG B:SER864 4.1 37.5 1.0
CG B:ASN868 4.1 36.5 1.0
N B:ASN767 4.2 23.1 1.0
CAE B:XAV1103 4.2 61.0 1.0
CB B:ASP766 4.2 32.0 1.0
CA B:ASN767 4.2 22.2 1.0
CB B:ASN767 4.3 19.9 1.0
C B:ASP766 4.4 27.7 1.0
O B:HOH1201 4.4 12.9 1.0
OD1 B:ASN868 4.5 29.6 1.0
O B:ASP766 4.6 26.4 1.0
CAF B:XAV1103 4.8 63.0 1.0
OD2 B:ASP770 4.8 60.7 1.0
O B:GLU763 4.8 39.8 1.0
CA B:ASP766 5.0 28.9 1.0

Reference:

A.G.Thorsell, T.Ekblad, T.Karlberg, M.Low, A.F.Pinto, L.Tresaugues, M.Moche, M.S.Cohen, H.Schuler. Structural Basis For Potency and Promiscuity in Poly(Adp-Ribose) Polymerase (Parp) and Tankyrase Inhibitors. J.Med.Chem. 2016.
ISSN: ISSN 0022-2623
PubMed: 28001384
Page generated: Thu Aug 1 05:31:48 2024

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