Fluorine in PDB 6zvl: ARUK3000263 Complex with Notum
Enzymatic activity of ARUK3000263 Complex with Notum
All present enzymatic activity of ARUK3000263 Complex with Notum:
3.1.1.98;
Protein crystallography data
The structure of ARUK3000263 Complex with Notum, PDB code: 6zvl
was solved by
Y.Zhao,
R.Ruza,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
52.83 /
1.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.805,
71.791,
78.036,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.1 /
22.3
|
Other elements in 6zvl:
The structure of ARUK3000263 Complex with Notum also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the ARUK3000263 Complex with Notum
(pdb code 6zvl). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
ARUK3000263 Complex with Notum, PDB code: 6zvl:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6zvl
Go back to
Fluorine Binding Sites List in 6zvl
Fluorine binding site 1 out
of 3 in the ARUK3000263 Complex with Notum
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of ARUK3000263 Complex with Notum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F509
b:0.8
occ:1.00
|
F14
|
A:QR2509
|
0.0
|
0.8
|
1.0
|
C13
|
A:QR2509
|
1.4
|
50.9
|
1.0
|
F15
|
A:QR2509
|
2.0
|
0.8
|
1.0
|
C12
|
A:QR2509
|
2.2
|
93.5
|
1.0
|
C17
|
A:QR2509
|
2.4
|
73.0
|
1.0
|
F16
|
A:QR2509
|
2.6
|
89.4
|
1.0
|
HG21
|
A:VAL187
|
2.7
|
15.9
|
1.0
|
HD11
|
A:ILE291
|
3.1
|
19.5
|
0.6
|
HE1
|
A:TYR129
|
3.3
|
27.8
|
1.0
|
HG11
|
A:VAL187
|
3.4
|
23.3
|
1.0
|
C10
|
A:QR2509
|
3.5
|
33.2
|
1.0
|
CG2
|
A:VAL187
|
3.5
|
13.2
|
1.0
|
HG22
|
A:VAL187
|
3.5
|
15.9
|
1.0
|
HD2
|
A:PHE319
|
3.6
|
20.5
|
1.0
|
HG21
|
A:THR236
|
3.7
|
12.6
|
1.0
|
C01
|
A:QR2509
|
3.8
|
34.7
|
1.0
|
HD1
|
A:TYR129
|
3.8
|
23.0
|
1.0
|
HD11
|
A:ILE291
|
3.8
|
18.9
|
0.4
|
CE1
|
A:TYR129
|
3.9
|
23.2
|
1.0
|
HG13
|
A:VAL187
|
3.9
|
23.3
|
1.0
|
CD1
|
A:ILE291
|
4.0
|
16.2
|
0.6
|
CG1
|
A:VAL187
|
4.0
|
19.4
|
1.0
|
HG12
|
A:ILE291
|
4.1
|
30.6
|
0.4
|
HD12
|
A:ILE291
|
4.1
|
19.5
|
0.6
|
CD1
|
A:TYR129
|
4.1
|
19.1
|
1.0
|
HG23
|
A:VAL187
|
4.2
|
15.9
|
1.0
|
HG13
|
A:ILE291
|
4.3
|
29.8
|
0.6
|
HD13
|
A:ILE291
|
4.3
|
18.9
|
0.4
|
CB
|
A:VAL187
|
4.3
|
12.8
|
1.0
|
CL1
|
A:QR2509
|
4.4
|
56.6
|
1.0
|
HB3
|
A:PHE319
|
4.4
|
15.7
|
1.0
|
HE2
|
A:PHE268
|
4.4
|
17.6
|
1.0
|
CD1
|
A:ILE291
|
4.4
|
15.8
|
0.4
|
OG1
|
A:THR236
|
4.5
|
11.5
|
1.0
|
HB
|
A:THR236
|
4.5
|
13.3
|
1.0
|
C09
|
A:QR2509
|
4.5
|
25.1
|
1.0
|
CD2
|
A:PHE319
|
4.5
|
17.1
|
1.0
|
HD2
|
A:PHE268
|
4.6
|
15.7
|
1.0
|
HA
|
A:ALA233
|
4.6
|
13.0
|
1.0
|
HD13
|
A:ILE291
|
4.6
|
19.5
|
0.6
|
CG2
|
A:THR236
|
4.6
|
10.4
|
1.0
|
O07
|
A:QR2509
|
4.6
|
33.1
|
1.0
|
CG1
|
A:ILE291
|
4.6
|
24.8
|
0.6
|
C08
|
A:QR2509
|
4.6
|
23.9
|
1.0
|
C02
|
A:QR2509
|
4.7
|
26.9
|
1.0
|
CG1
|
A:ILE291
|
4.7
|
25.5
|
0.4
|
HB
|
A:VAL187
|
4.7
|
15.4
|
1.0
|
CB
|
A:THR236
|
4.8
|
11.1
|
1.0
|
CZ
|
A:TYR129
|
4.8
|
30.2
|
1.0
|
HG12
|
A:ILE291
|
4.9
|
29.8
|
0.6
|
HG12
|
A:VAL187
|
4.9
|
23.3
|
1.0
|
HG1
|
A:THR236
|
4.9
|
13.8
|
1.0
|
CE2
|
A:PHE268
|
4.9
|
14.7
|
1.0
|
HG13
|
A:ILE291
|
4.9
|
30.6
|
0.4
|
CD2
|
A:PHE268
|
5.0
|
13.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6zvl
Go back to
Fluorine Binding Sites List in 6zvl
Fluorine binding site 2 out
of 3 in the ARUK3000263 Complex with Notum
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of ARUK3000263 Complex with Notum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F509
b:0.8
occ:1.00
|
F15
|
A:QR2509
|
0.0
|
0.8
|
1.0
|
C13
|
A:QR2509
|
1.4
|
50.9
|
1.0
|
F14
|
A:QR2509
|
2.0
|
0.8
|
1.0
|
F16
|
A:QR2509
|
2.0
|
89.4
|
1.0
|
HD13
|
A:ILE291
|
2.4
|
18.9
|
0.4
|
HD11
|
A:ILE291
|
2.4
|
18.9
|
0.4
|
HD11
|
A:ILE291
|
2.6
|
19.5
|
0.6
|
HG13
|
A:ILE291
|
2.7
|
29.8
|
0.6
|
CD1
|
A:ILE291
|
2.8
|
15.8
|
0.4
|
HD2
|
A:PHE319
|
2.8
|
20.5
|
1.0
|
C12
|
A:QR2509
|
2.8
|
93.5
|
1.0
|
HB3
|
A:PHE319
|
2.8
|
15.7
|
1.0
|
HG12
|
A:ILE291
|
3.0
|
30.6
|
0.4
|
CD1
|
A:ILE291
|
3.2
|
16.2
|
0.6
|
HD12
|
A:ILE291
|
3.3
|
19.5
|
0.6
|
CG1
|
A:ILE291
|
3.4
|
24.8
|
0.6
|
CG1
|
A:ILE291
|
3.4
|
25.5
|
0.4
|
CL1
|
A:QR2509
|
3.5
|
56.6
|
1.0
|
C10
|
A:QR2509
|
3.5
|
33.2
|
1.0
|
CD2
|
A:PHE319
|
3.5
|
17.1
|
1.0
|
HD12
|
A:ILE291
|
3.6
|
18.9
|
0.4
|
CB
|
A:PHE319
|
3.6
|
13.1
|
1.0
|
HG21
|
A:THR236
|
3.7
|
12.6
|
1.0
|
HG21
|
A:VAL187
|
3.7
|
15.9
|
1.0
|
HG12
|
A:ILE291
|
3.8
|
29.8
|
0.6
|
C17
|
A:QR2509
|
3.8
|
73.0
|
1.0
|
HG13
|
A:ILE291
|
3.9
|
30.6
|
0.4
|
HB2
|
A:PHE319
|
3.9
|
15.7
|
1.0
|
HG11
|
A:VAL187
|
3.9
|
23.3
|
1.0
|
CG
|
A:PHE319
|
4.0
|
12.8
|
1.0
|
HG21
|
A:ILE291
|
4.1
|
26.2
|
0.4
|
HG21
|
A:ILE291
|
4.1
|
27.6
|
0.6
|
HD13
|
A:ILE291
|
4.1
|
19.5
|
0.6
|
O
|
A:PHE319
|
4.3
|
13.8
|
1.0
|
HE1
|
A:TYR129
|
4.5
|
27.8
|
1.0
|
CE2
|
A:PHE319
|
4.6
|
14.3
|
1.0
|
CB
|
A:ILE291
|
4.6
|
29.6
|
0.6
|
HD2
|
A:PHE268
|
4.6
|
15.7
|
1.0
|
CG2
|
A:THR236
|
4.6
|
10.4
|
1.0
|
CB
|
A:ILE291
|
4.7
|
14.5
|
0.4
|
CG2
|
A:VAL187
|
4.7
|
13.2
|
1.0
|
HE2
|
A:PHE319
|
4.7
|
17.1
|
1.0
|
CG2
|
A:ILE291
|
4.7
|
21.8
|
0.4
|
CG2
|
A:ILE291
|
4.7
|
23.0
|
0.6
|
HB3
|
A:PRO287
|
4.8
|
47.3
|
1.0
|
CA
|
A:PHE319
|
4.8
|
11.4
|
1.0
|
CG1
|
A:VAL187
|
4.8
|
19.4
|
1.0
|
C
|
A:PHE319
|
4.8
|
12.4
|
1.0
|
C09
|
A:QR2509
|
4.9
|
25.1
|
1.0
|
HG23
|
A:ILE291
|
4.9
|
26.2
|
0.4
|
HG23
|
A:ILE291
|
4.9
|
27.6
|
0.6
|
HG23
|
A:THR236
|
4.9
|
12.6
|
1.0
|
CE1
|
A:TYR129
|
5.0
|
23.2
|
1.0
|
HB
|
A:ILE291
|
5.0
|
35.5
|
0.6
|
|
Fluorine binding site 3 out
of 3 in 6zvl
Go back to
Fluorine Binding Sites List in 6zvl
Fluorine binding site 3 out
of 3 in the ARUK3000263 Complex with Notum
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of ARUK3000263 Complex with Notum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F509
b:89.4
occ:1.00
|
F16
|
A:QR2509
|
0.0
|
89.4
|
1.0
|
C13
|
A:QR2509
|
1.4
|
50.9
|
1.0
|
F15
|
A:QR2509
|
2.0
|
0.8
|
1.0
|
C12
|
A:QR2509
|
2.2
|
93.5
|
1.0
|
F14
|
A:QR2509
|
2.6
|
0.8
|
1.0
|
HD2
|
A:PHE268
|
2.6
|
15.7
|
1.0
|
C10
|
A:QR2509
|
2.8
|
33.2
|
1.0
|
CL1
|
A:QR2509
|
2.9
|
56.6
|
1.0
|
HG21
|
A:THR236
|
3.1
|
12.6
|
1.0
|
C17
|
A:QR2509
|
3.2
|
73.0
|
1.0
|
HB3
|
A:PHE319
|
3.3
|
15.7
|
1.0
|
CD2
|
A:PHE268
|
3.3
|
13.1
|
1.0
|
O
|
A:PHE319
|
3.4
|
13.8
|
1.0
|
HB2
|
A:PHE268
|
3.7
|
15.6
|
1.0
|
HD11
|
A:ILE291
|
3.7
|
18.9
|
0.4
|
HG1
|
A:THR236
|
3.8
|
13.8
|
1.0
|
HE2
|
A:PHE268
|
3.8
|
17.6
|
1.0
|
HD13
|
A:ILE291
|
3.8
|
18.9
|
0.4
|
OG1
|
A:THR236
|
3.9
|
11.5
|
1.0
|
CG2
|
A:THR236
|
3.9
|
10.4
|
1.0
|
CE2
|
A:PHE268
|
4.0
|
14.7
|
1.0
|
HG23
|
A:THR236
|
4.0
|
12.6
|
1.0
|
HD2
|
A:PHE319
|
4.0
|
20.5
|
1.0
|
C09
|
A:QR2509
|
4.0
|
25.1
|
1.0
|
O
|
A:HOH628
|
4.1
|
12.3
|
1.0
|
CG
|
A:PHE268
|
4.3
|
12.6
|
1.0
|
CD1
|
A:ILE291
|
4.3
|
15.8
|
0.4
|
CB
|
A:PHE319
|
4.3
|
13.1
|
1.0
|
C
|
A:PHE319
|
4.3
|
12.4
|
1.0
|
C01
|
A:QR2509
|
4.4
|
34.7
|
1.0
|
HG13
|
A:ILE291
|
4.4
|
29.8
|
0.6
|
CB
|
A:PHE268
|
4.4
|
13.0
|
1.0
|
CB
|
A:THR236
|
4.5
|
11.1
|
1.0
|
HG11
|
A:VAL187
|
4.5
|
23.3
|
1.0
|
HD11
|
A:ILE291
|
4.6
|
19.5
|
0.6
|
HB2
|
A:PHE319
|
4.7
|
15.7
|
1.0
|
HG22
|
A:THR236
|
4.7
|
12.6
|
1.0
|
C08
|
A:QR2509
|
4.7
|
23.9
|
1.0
|
HB
|
A:THR236
|
4.7
|
13.3
|
1.0
|
HA
|
A:PHE320
|
4.8
|
14.9
|
1.0
|
HB3
|
A:PHE268
|
4.8
|
15.6
|
1.0
|
CD2
|
A:PHE319
|
4.8
|
17.1
|
1.0
|
CA
|
A:PHE319
|
4.9
|
11.4
|
1.0
|
HD12
|
A:ILE291
|
4.9
|
18.9
|
0.4
|
HG21
|
A:VAL187
|
5.0
|
15.9
|
1.0
|
HG12
|
A:ILE291
|
5.0
|
30.6
|
0.4
|
CE1
|
A:PHE320
|
5.0
|
16.2
|
1.0
|
|
Reference:
W.Mahy,
N.J.Willis,
Y.Zhao,
H.L.Woodward,
F.Svensson,
J.Sipthorp,
L.Vecchia,
R.R.Ruza,
J.Hillier,
S.Kjaer,
S.Frew,
A.Monaghan,
M.Bictash,
P.C.Salinas,
P.Whiting,
J.P.Vincent,
E.Y.Jones,
P.V.Fish.
5-Phenyl-1,3,4-Oxadiazol-2(3 H )-Ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified By the Optimization of A Crystallographic Fragment Screening Hit. J.Med.Chem. V. 63 12942 2020.
ISSN: ISSN 0022-2623
PubMed: 33124429
DOI: 10.1021/ACS.JMEDCHEM.0C01391
Page generated: Fri Aug 2 05:26:26 2024
|