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Fluorine in PDB 6j20: Crystal Structure of the Human NK1 Substance P Receptor

Enzymatic activity of Crystal Structure of the Human NK1 Substance P Receptor

All present enzymatic activity of Crystal Structure of the Human NK1 Substance P Receptor:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of the Human NK1 Substance P Receptor, PDB code: 6j20 was solved by S.Chen, M.Lu, H.Zhang, B.Wu, Q.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 2.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 102.512, 102.512, 156.962, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human NK1 Substance P Receptor (pdb code 6j20). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of the Human NK1 Substance P Receptor, PDB code: 6j20:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 1 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:0.8
occ:1.00
 F10 A:GBQ1201 0.0 0.8 1.0
C09 A:GBQ1201 1.4 0.6 1.0
F11 A:GBQ1201 2.3 0.2 1.0
F12 A:GBQ1201 2.3 0.5 1.0
C07 A:GBQ1201 2.3 99.9 1.0
C08 A:GBQ1201 2.9 97.8 1.0
C06 A:GBQ1201 3.3 96.7 1.0
CB A:PRO112 3.6 93.1 1.0
CG A:PRO112 3.7 98.7 1.0
ND2 A:ASN89 3.8 0.8 1.0
SD A:MET295 4.1 0.0 1.0
C03 A:GBQ1201 4.2 95.5 1.0
C05 A:GBQ1201 4.5 94.8 1.0
CB A:ASN85 4.5 0.9 1.0
CG A:ASN89 4.5 0.2 1.0
CE A:MET295 4.6 0.1 1.0
SD A:MET81 4.6 0.1 1.0
CG A:MET295 4.7 0.0 1.0
CG A:ASN85 4.7 0.9 1.0
OD1 A:ASN89 4.8 1.0 1.0
C04 A:GBQ1201 4.8 94.9 1.0
CA A:PRO112 4.9 92.3 1.0

Fluorine binding site 2 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 2 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:0.2
occ:1.00
 F11 A:GBQ1201 0.0 0.2 1.0
C09 A:GBQ1201 1.4 0.6 1.0
F12 A:GBQ1201 2.3 0.5 1.0
F10 A:GBQ1201 2.3 0.8 1.0
C07 A:GBQ1201 2.3 99.9 1.0
C08 A:GBQ1201 2.8 97.8 1.0
ND2 A:ASN89 3.4 0.8 1.0
C06 A:GBQ1201 3.6 96.7 1.0
CE1 A:PHE264 3.6 90.2 1.0
CG A:MET291 3.9 0.4 1.0
CZ A:PHE264 3.9 88.3 1.0
C03 A:GBQ1201 4.2 95.5 1.0
SD A:MET291 4.2 0.3 1.0
OH A:TYR287 4.5 0.3 1.0
CG A:ASN89 4.6 0.2 1.0
CD1 A:PHE264 4.7 89.9 1.0
CG A:MET295 4.7 0.0 1.0
C05 A:GBQ1201 4.7 94.8 1.0
SD A:MET295 4.8 0.0 1.0
C04 A:GBQ1201 4.9 94.9 1.0

Fluorine binding site 3 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 3 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:0.5
occ:1.00
 F12 A:GBQ1201 0.0 0.5 1.0
C09 A:GBQ1201 1.4 0.6 1.0
F11 A:GBQ1201 2.3 0.2 1.0
F10 A:GBQ1201 2.3 0.8 1.0
C07 A:GBQ1201 2.3 99.9 1.0
C06 A:GBQ1201 2.7 96.7 1.0
CH2 A:TRP261 3.1 92.1 1.0
CZ3 A:TRP261 3.6 90.3 1.0
C08 A:GBQ1201 3.6 97.8 1.0
CE1 A:PHE264 4.0 90.2 1.0
CG A:MET295 4.1 0.0 1.0
C05 A:GBQ1201 4.1 94.8 1.0
CZ A:PHE264 4.2 88.3 1.0
CZ2 A:TRP261 4.3 91.9 1.0
CB A:ALA294 4.3 0.8 1.0
SD A:MET295 4.5 0.0 1.0
F15 A:GBQ1201 4.6 92.2 1.0
CD1 A:PHE264 4.7 89.9 1.0
SD A:MET81 4.7 0.1 1.0
C03 A:GBQ1201 4.7 95.5 1.0
CE A:MET295 4.8 0.1 1.0
CB A:PRO112 4.9 93.1 1.0
CE3 A:TRP261 4.9 88.1 1.0
C04 A:GBQ1201 4.9 94.9 1.0
CE2 A:PHE264 5.0 89.6 1.0
C13 A:GBQ1201 5.0 93.7 1.0
N A:MET295 5.0 0.9 1.0

Fluorine binding site 4 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 4 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:93.8
occ:1.00
 F14 A:GBQ1201 0.0 93.8 1.0
C13 A:GBQ1201 1.3 93.7 1.0
F16 A:GBQ1201 2.1 94.4 1.0
F15 A:GBQ1201 2.1 92.2 1.0
C05 A:GBQ1201 2.2 94.8 1.0
C04 A:GBQ1201 2.8 94.9 1.0
C34 A:GBQ1201 3.1 87.1 1.0
F37 A:GBQ1201 3.2 88.3 1.0
C35 A:GBQ1201 3.2 86.6 1.0
C06 A:GBQ1201 3.4 96.7 1.0
CD1 A:ILE204 3.5 90.0 1.0
CE2 A:PHE264 3.6 89.6 1.0
C33 A:GBQ1201 3.7 85.0 1.0
C36 A:GBQ1201 4.0 88.2 1.0
CE1 A:HIS265 4.1 89.3 1.0
C03 A:GBQ1201 4.1 95.5 1.0
CZ A:PHE264 4.3 88.3 1.0
C32 A:GBQ1201 4.4 87.0 1.0
CD2 A:PHE264 4.4 87.2 1.0
C31 A:GBQ1201 4.5 90.3 1.0
CG1 A:ILE113 4.6 87.6 1.0
C07 A:GBQ1201 4.6 99.9 1.0
CZ3 A:TRP261 4.7 90.3 1.0
CG1 A:ILE204 4.8 87.5 1.0
C08 A:GBQ1201 4.8 97.8 1.0
NE2 A:HIS265 4.9 89.5 1.0
ND1 A:HIS265 4.9 90.4 1.0
O17 A:GBQ1201 5.0 94.6 1.0

Fluorine binding site 5 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 5 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:92.2
occ:1.00
 F15 A:GBQ1201 0.0 92.2 1.0
C13 A:GBQ1201 1.3 93.7 1.0
F14 A:GBQ1201 2.1 93.8 1.0
F16 A:GBQ1201 2.2 94.4 1.0
C05 A:GBQ1201 2.3 94.8 1.0
C06 A:GBQ1201 2.6 96.7 1.0
CZ3 A:TRP261 3.2 90.3 1.0
CG2 A:VAL116 3.4 89.5 1.0
CH2 A:TRP261 3.4 92.1 1.0
C04 A:GBQ1201 3.6 94.9 1.0
CD1 A:ILE204 3.6 90.0 1.0
CE3 A:TRP261 3.9 88.1 1.0
CB A:VAL116 3.9 89.0 1.0
C07 A:GBQ1201 4.0 99.9 1.0
CE2 A:PHE264 4.1 89.6 1.0
CZ2 A:TRP261 4.2 91.9 1.0
CG1 A:VAL116 4.2 87.6 1.0
O A:PRO112 4.5 94.2 1.0
CZ A:PHE264 4.6 88.3 1.0
CD2 A:TRP261 4.6 87.3 1.0
F12 A:GBQ1201 4.6 0.5 1.0
CD2 A:PHE264 4.6 87.2 1.0
C03 A:GBQ1201 4.7 95.5 1.0
CE2 A:TRP261 4.7 91.7 1.0
CE1 A:HIS265 4.8 89.3 1.0
C A:PRO112 4.9 94.6 1.0
C08 A:GBQ1201 4.9 97.8 1.0
C09 A:GBQ1201 4.9 0.6 1.0
NE2 A:HIS265 5.0 89.5 1.0

Fluorine binding site 6 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 6 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


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 Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:94.4
occ:1.00
 F16 A:GBQ1201 0.0 94.4 1.0
C13 A:GBQ1201 1.3 93.7 1.0
F14 A:GBQ1201 2.1 93.8 1.0
F15 A:GBQ1201 2.2 92.2 1.0
C05 A:GBQ1201 2.2 94.8 1.0
C04 A:GBQ1201 2.9 94.9 1.0
C06 A:GBQ1201 3.3 96.7 1.0
CA A:ILE113 3.3 87.5 1.0
CG1 A:ILE113 3.4 87.6 1.0
N A:ILE113 3.4 89.7 1.0
CD1 A:ILE204 3.5 90.0 1.0
C A:PRO112 3.5 94.6 1.0
O A:PRO112 3.6 94.2 1.0
CB A:ILE113 3.9 89.3 1.0
CG2 A:VAL116 4.1 89.5 1.0
C03 A:GBQ1201 4.2 95.5 1.0
CB A:PRO112 4.2 93.1 1.0
CB A:VAL116 4.3 89.0 1.0
C A:ILE113 4.5 92.1 1.0
C07 A:GBQ1201 4.5 99.9 1.0
CA A:PRO112 4.5 92.3 1.0
F37 A:GBQ1201 4.6 88.3 1.0
C34 A:GBQ1201 4.6 87.1 1.0
CD1 A:ILE113 4.7 89.2 1.0
O A:ILE113 4.7 90.7 1.0
CG2 A:ILE113 4.8 88.5 1.0
C33 A:GBQ1201 4.8 85.0 1.0
C08 A:GBQ1201 4.8 97.8 1.0
CG1 A:ILE204 5.0 87.5 1.0

Fluorine binding site 7 out of 7 in 6j20

Go back to Fluorine Binding Sites List in 6j20
Fluorine binding site 7 out of 7 in the Crystal Structure of the Human NK1 Substance P Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Human NK1 Substance P Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1201

b:88.3
occ:1.00
 F37 A:GBQ1201 0.0 88.3 1.0
C34 A:GBQ1201 1.4 87.1 1.0
C33 A:GBQ1201 2.4 85.0 1.0
C35 A:GBQ1201 2.4 86.6 1.0
F14 A:GBQ1201 3.2 93.8 1.0
CG1 A:VAL200 3.3 94.4 1.0
OG1 A:THR201 3.5 95.6 1.0
C32 A:GBQ1201 3.7 87.0 1.0
CE1 A:HIS265 3.7 89.3 1.0
C36 A:GBQ1201 3.7 88.2 1.0
CD1 A:ILE204 3.9 90.0 1.0
ND1 A:HIS265 4.0 90.4 1.0
N A:THR201 4.0 88.5 1.0
CB A:VAL200 4.1 94.7 1.0
C31 A:GBQ1201 4.2 90.3 1.0
CA A:THR201 4.2 87.5 1.0
CE1 A:HIS197 4.3 96.1 1.0
ND1 A:HIS197 4.4 97.3 1.0
C A:VAL200 4.4 93.0 1.0
C13 A:GBQ1201 4.4 93.7 1.0
CG1 A:ILE204 4.4 87.5 1.0
CB A:THR201 4.5 93.6 1.0
O A:HIS197 4.6 94.9 1.0
F16 A:GBQ1201 4.6 94.4 1.0
O A:VAL200 4.9 92.9 1.0
CA A:VAL200 4.9 91.2 1.0
NE2 A:HIS265 4.9 89.5 1.0

Reference:

S.Chen, M.Lu, D.Liu, L.Yang, C.Yi, L.Ma, H.Zhang, Q.Liu, T.M.Frimurer, M.W.Wang, T.W.Schwartz, R.C.Stevens, B.Wu, K.Wuthrich, Q.Zhao. Human Substance P Receptor Binding Mode of the Antagonist Drug Aprepitant By uc(Nmr) and Crystallography. Nat Commun V. 10 638 2019.
ISSN: ESSN 2041-1723
PubMed: 30733446
DOI: 10.1038/S41467-019-08568-5
Page generated: Thu Aug 1 21:28:03 2024

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