Fluorine in PDB 6hlp: Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
Protein crystallography data
The structure of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant, PDB code: 6hlp
was solved by
J.Schoppe,
J.Ehrenmann,
C.Klenk,
P.Rucktooa,
M.Schutz,
A.S.Dore,
A.Pluckthun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.24 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.658,
76.571,
166.035,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
22.5
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
(pdb code 6hlp). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant, PDB code: 6hlp:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:54.6
occ:1.00
|
F28
|
A:GAW1501
|
0.0
|
54.6
|
1.0
|
C27
|
A:GAW1501
|
1.3
|
54.4
|
1.0
|
F29
|
A:GAW1501
|
2.1
|
54.1
|
1.0
|
F30
|
A:GAW1501
|
2.1
|
58.5
|
1.0
|
C25
|
A:GAW1501
|
2.4
|
47.8
|
1.0
|
ND2
|
A:ASN89
|
3.0
|
63.7
|
1.0
|
C26
|
A:GAW1501
|
3.1
|
43.6
|
1.0
|
C24
|
A:GAW1501
|
3.4
|
44.1
|
1.0
|
SD
|
A:MET295
|
3.4
|
68.2
|
1.0
|
CB
|
A:PRO112
|
3.6
|
42.9
|
1.0
|
CG
|
A:PRO112
|
3.7
|
41.6
|
1.0
|
O
|
A:HOH1646
|
3.8
|
55.4
|
1.0
|
CE
|
A:MET295
|
4.2
|
70.0
|
1.0
|
CG
|
A:ASN89
|
4.2
|
59.1
|
1.0
|
C21
|
A:GAW1501
|
4.4
|
44.3
|
1.0
|
SD
|
A:MET81
|
4.4
|
57.1
|
1.0
|
C23
|
A:GAW1501
|
4.6
|
44.0
|
1.0
|
CE
|
A:MET81
|
4.6
|
60.0
|
1.0
|
OD1
|
A:ASN89
|
4.8
|
60.9
|
1.0
|
CB
|
A:ASN85
|
4.8
|
43.4
|
1.0
|
CG
|
A:MET81
|
4.9
|
52.6
|
1.0
|
CA
|
A:PRO112
|
5.0
|
39.1
|
1.0
|
C22
|
A:GAW1501
|
5.0
|
42.9
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:54.1
occ:1.00
|
F29
|
A:GAW1501
|
0.0
|
54.1
|
1.0
|
C27
|
A:GAW1501
|
1.3
|
54.4
|
1.0
|
F30
|
A:GAW1501
|
2.1
|
58.5
|
1.0
|
F28
|
A:GAW1501
|
2.1
|
54.6
|
1.0
|
C25
|
A:GAW1501
|
2.4
|
47.8
|
1.0
|
C24
|
A:GAW1501
|
2.8
|
44.1
|
1.0
|
SD
|
A:MET295
|
3.2
|
68.2
|
1.0
|
CH2
|
A:TRP261
|
3.4
|
36.8
|
1.0
|
C26
|
A:GAW1501
|
3.7
|
43.6
|
1.0
|
CZ3
|
A:TRP261
|
3.9
|
37.7
|
1.0
|
C23
|
A:GAW1501
|
4.1
|
44.0
|
1.0
|
CZ
|
A:PHE264
|
4.2
|
41.4
|
1.0
|
CE2
|
A:PHE264
|
4.2
|
42.1
|
1.0
|
CE
|
A:MET81
|
4.3
|
60.0
|
1.0
|
CG
|
A:MET295
|
4.5
|
56.9
|
1.0
|
CZ2
|
A:TRP261
|
4.5
|
38.2
|
1.0
|
CE
|
A:MET295
|
4.6
|
70.0
|
1.0
|
ND2
|
A:ASN89
|
4.6
|
63.7
|
1.0
|
SD
|
A:MET81
|
4.7
|
57.1
|
1.0
|
CB
|
A:PRO112
|
4.7
|
42.9
|
1.0
|
CB
|
A:ALA294
|
4.8
|
38.3
|
1.0
|
C21
|
A:GAW1501
|
4.9
|
44.3
|
1.0
|
CE1
|
A:PHE264
|
5.0
|
41.6
|
1.0
|
C22
|
A:GAW1501
|
5.0
|
42.9
|
1.0
|
CD2
|
A:PHE264
|
5.0
|
39.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:58.5
occ:1.00
|
F30
|
A:GAW1501
|
0.0
|
58.5
|
1.0
|
C27
|
A:GAW1501
|
1.3
|
54.4
|
1.0
|
F29
|
A:GAW1501
|
2.1
|
54.1
|
1.0
|
F28
|
A:GAW1501
|
2.1
|
54.6
|
1.0
|
C25
|
A:GAW1501
|
2.4
|
47.8
|
1.0
|
C26
|
A:GAW1501
|
3.0
|
43.6
|
1.0
|
ND2
|
A:ASN89
|
3.5
|
63.7
|
1.0
|
C24
|
A:GAW1501
|
3.5
|
44.1
|
1.0
|
SD
|
A:MET295
|
3.7
|
68.2
|
1.0
|
CE2
|
A:PHE264
|
3.9
|
42.1
|
1.0
|
CZ
|
A:PHE264
|
4.0
|
41.4
|
1.0
|
SD
|
A:MET291
|
4.1
|
59.2
|
1.0
|
CG
|
A:MET291
|
4.2
|
49.5
|
1.0
|
C21
|
A:GAW1501
|
4.4
|
44.3
|
1.0
|
O
|
A:HOH1646
|
4.4
|
55.4
|
1.0
|
CG
|
A:ASN89
|
4.4
|
59.1
|
1.0
|
C23
|
A:GAW1501
|
4.7
|
44.0
|
1.0
|
CG
|
A:MET295
|
4.8
|
56.9
|
1.0
|
CB
|
A:ASN89
|
4.9
|
53.1
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:48.3
occ:1.00
|
F32
|
A:GAW1501
|
0.0
|
48.3
|
1.0
|
C31
|
A:GAW1501
|
1.3
|
47.2
|
1.0
|
F33
|
A:GAW1501
|
2.1
|
49.5
|
1.0
|
F34
|
A:GAW1501
|
2.1
|
50.2
|
1.0
|
C23
|
A:GAW1501
|
2.4
|
44.0
|
1.0
|
C24
|
A:GAW1501
|
3.0
|
44.1
|
1.0
|
CE1
|
A:PHE264
|
3.4
|
41.6
|
1.0
|
C22
|
A:GAW1501
|
3.5
|
42.9
|
1.0
|
CZ3
|
A:TRP261
|
3.5
|
37.7
|
1.0
|
CD1
|
A:ILE204
|
3.7
|
37.9
|
1.0
|
CE1
|
A:HIS265
|
3.7
|
41.5
|
1.0
|
C05
|
A:GAW1501
|
3.9
|
52.5
|
1.0
|
C04
|
A:GAW1501
|
3.9
|
54.1
|
1.0
|
CD1
|
A:PHE264
|
4.0
|
37.6
|
1.0
|
CE3
|
A:TRP261
|
4.1
|
39.6
|
1.0
|
CH2
|
A:TRP261
|
4.1
|
36.8
|
1.0
|
CZ
|
A:PHE264
|
4.2
|
41.4
|
1.0
|
C25
|
A:GAW1501
|
4.3
|
47.8
|
1.0
|
NE2
|
A:HIS265
|
4.4
|
40.0
|
1.0
|
ND1
|
A:HIS265
|
4.6
|
41.4
|
1.0
|
C21
|
A:GAW1501
|
4.7
|
44.3
|
1.0
|
C06
|
A:GAW1501
|
4.8
|
50.0
|
1.0
|
C03
|
A:GAW1501
|
4.8
|
52.3
|
1.0
|
O
|
A:HOH1661
|
4.9
|
36.6
|
1.0
|
C26
|
A:GAW1501
|
5.0
|
43.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:49.5
occ:1.00
|
F33
|
A:GAW1501
|
0.0
|
49.5
|
1.0
|
C31
|
A:GAW1501
|
1.3
|
47.2
|
1.0
|
F34
|
A:GAW1501
|
2.1
|
50.2
|
1.0
|
F32
|
A:GAW1501
|
2.1
|
48.3
|
1.0
|
C23
|
A:GAW1501
|
2.4
|
44.0
|
1.0
|
C22
|
A:GAW1501
|
2.8
|
42.9
|
1.0
|
C04
|
A:GAW1501
|
3.0
|
54.1
|
1.0
|
C03
|
A:GAW1501
|
3.4
|
52.3
|
1.0
|
CD1
|
A:ILE204
|
3.5
|
37.9
|
1.0
|
C05
|
A:GAW1501
|
3.6
|
52.5
|
1.0
|
CG1
|
A:ILE113
|
3.6
|
45.1
|
1.0
|
C24
|
A:GAW1501
|
3.7
|
44.1
|
1.0
|
C21
|
A:GAW1501
|
4.2
|
44.3
|
1.0
|
C02
|
A:GAW1501
|
4.3
|
52.5
|
1.0
|
C06
|
A:GAW1501
|
4.4
|
50.0
|
1.0
|
CG1
|
A:VAL200
|
4.4
|
39.3
|
1.0
|
CD1
|
A:ILE113
|
4.5
|
45.7
|
1.0
|
CA
|
A:ILE113
|
4.5
|
37.5
|
1.0
|
CB
|
A:ILE113
|
4.6
|
44.4
|
1.0
|
CE1
|
A:HIS265
|
4.7
|
41.5
|
1.0
|
C07
|
A:GAW1501
|
4.7
|
51.3
|
1.0
|
CE1
|
A:PHE264
|
4.8
|
41.6
|
1.0
|
C25
|
A:GAW1501
|
4.8
|
47.8
|
1.0
|
CG1
|
A:ILE204
|
4.8
|
37.3
|
1.0
|
N
|
A:ILE113
|
4.8
|
40.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6hlp
Go back to
Fluorine Binding Sites List in 6hlp
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Neurokinin 1 Receptor in Complex with the Small Molecule Antagonist Netupitant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1501
b:50.2
occ:1.00
|
F34
|
A:GAW1501
|
0.0
|
50.2
|
1.0
|
C31
|
A:GAW1501
|
1.3
|
47.2
|
1.0
|
F33
|
A:GAW1501
|
2.1
|
49.5
|
1.0
|
F32
|
A:GAW1501
|
2.1
|
48.3
|
1.0
|
C23
|
A:GAW1501
|
2.4
|
44.0
|
1.0
|
C24
|
A:GAW1501
|
3.0
|
44.1
|
1.0
|
C22
|
A:GAW1501
|
3.5
|
42.9
|
1.0
|
CD1
|
A:ILE204
|
3.5
|
37.9
|
1.0
|
O
|
A:PRO112
|
3.6
|
36.5
|
1.0
|
CG1
|
A:ILE116
|
3.7
|
40.8
|
1.0
|
C
|
A:PRO112
|
3.8
|
43.1
|
1.0
|
CA
|
A:ILE113
|
3.9
|
37.5
|
1.0
|
CB
|
A:ILE116
|
4.0
|
40.0
|
1.0
|
N
|
A:ILE113
|
4.0
|
40.9
|
1.0
|
CG1
|
A:ILE113
|
4.2
|
45.1
|
1.0
|
C25
|
A:GAW1501
|
4.3
|
47.8
|
1.0
|
CB
|
A:PRO112
|
4.4
|
42.9
|
1.0
|
CH2
|
A:TRP261
|
4.5
|
36.8
|
1.0
|
CG2
|
A:ILE116
|
4.5
|
35.6
|
1.0
|
CZ3
|
A:TRP261
|
4.6
|
37.7
|
1.0
|
C21
|
A:GAW1501
|
4.7
|
44.3
|
1.0
|
CA
|
A:PRO112
|
4.7
|
39.1
|
1.0
|
CB
|
A:ILE113
|
4.7
|
44.4
|
1.0
|
C04
|
A:GAW1501
|
4.9
|
54.1
|
1.0
|
CG1
|
A:ILE204
|
4.9
|
37.3
|
1.0
|
C26
|
A:GAW1501
|
5.0
|
43.6
|
1.0
|
|
Reference:
J.Schoppe,
J.Ehrenmann,
C.Klenk,
P.Rucktooa,
M.Schutz,
A.S.Dore,
A.Pluckthun.
Crystal Structures of the Human Neurokinin 1 Receptor in Complex with Clinically Used Antagonists. Nat Commun V. 10 17 2019.
ISSN: ESSN 2041-1723
PubMed: 30604743
DOI: 10.1038/S41467-018-07939-8
Page generated: Thu Aug 1 21:12:15 2024
|