Atomistry » Fluorine » PDB 6i8z-6jsf » 6j21
Atomistry »
  Fluorine »
    PDB 6i8z-6jsf »
      6j21 »

Fluorine in PDB 6j21: 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: 6j21 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) 29.98 / 3.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.110, 103.110, 158.160, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human NK1 Substance P Receptor (pdb code 6j21). 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: 6j21:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.4
occ:1.00
 F10 A:GBQ1201 0.0 0.4 1.0
C09 A:GBQ1201 1.4 0.4 1.0
F11 A:GBQ1201 2.3 0.9 1.0
F12 A:GBQ1201 2.3 0.7 1.0
C07 A:GBQ1201 2.3 0.6 1.0
C08 A:GBQ1201 2.9 0.8 1.0
C06 A:GBQ1201 3.4 0.2 1.0
CB A:PRO112 3.7 99.6 1.0
CG A:PRO112 3.7 0.7 1.0
ND2 A:ASN89 4.0 0.0 1.0
OD1 A:ASN89 4.1 0.9 1.0
C03 A:GBQ1201 4.2 0.6 1.0
CG A:ASN89 4.2 0.3 1.0
SD A:MET295 4.4 0.5 1.0
CE A:MET295 4.5 0.6 1.0
OD1 A:ASN85 4.5 0.8 1.0
CB A:ASN85 4.5 0.1 1.0
C05 A:GBQ1201 4.5 0.4 1.0
CG A:ASN85 4.6 0.5 1.0
SD A:MET81 4.8 0.4 1.0
C04 A:GBQ1201 4.9 0.4 1.0
CG A:MET295 4.9 0.4 1.0
CA A:PRO112 5.0 98.6 1.0

Fluorine binding site 2 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.9
occ:1.00
 F11 A:GBQ1201 0.0 0.9 1.0
C09 A:GBQ1201 1.4 0.4 1.0
F10 A:GBQ1201 2.3 0.4 1.0
F12 A:GBQ1201 2.3 0.7 1.0
C07 A:GBQ1201 2.3 0.6 1.0
C08 A:GBQ1201 2.8 0.8 1.0
CE1 A:PHE264 3.4 0.2 1.0
C06 A:GBQ1201 3.5 0.2 1.0
CZ A:PHE264 3.6 0.3 1.0
ND2 A:ASN89 3.9 0.0 1.0
CG A:MET291 4.0 0.5 1.0
OH A:TYR287 4.1 0.3 1.0
C03 A:GBQ1201 4.2 0.6 1.0
SD A:MET291 4.3 0.6 1.0
CD1 A:PHE264 4.5 0.7 1.0
CG A:ASN89 4.6 0.3 1.0
C05 A:GBQ1201 4.6 0.4 1.0
CE2 A:PHE264 4.8 0.7 1.0
C04 A:GBQ1201 4.9 0.4 1.0

Fluorine binding site 3 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.7
occ:1.00
 F12 A:GBQ1201 0.0 0.7 1.0
C09 A:GBQ1201 1.4 0.4 1.0
F10 A:GBQ1201 2.3 0.4 1.0
F11 A:GBQ1201 2.3 0.9 1.0
C07 A:GBQ1201 2.4 0.6 1.0
C06 A:GBQ1201 2.7 0.2 1.0
CH2 A:TRP261 3.3 0.1 1.0
C08 A:GBQ1201 3.7 0.8 1.0
CZ3 A:TRP261 3.8 0.0 1.0
C05 A:GBQ1201 4.1 0.4 1.0
CG A:MET295 4.2 0.4 1.0
CE1 A:PHE264 4.2 0.2 1.0
CZ A:PHE264 4.3 0.3 1.0
CZ2 A:TRP261 4.3 0.6 1.0
CE A:MET295 4.3 0.6 1.0
SD A:MET295 4.4 0.5 1.0
SD A:MET81 4.6 0.4 1.0
F15 A:GBQ1201 4.6 0.5 1.0
CB A:ALA294 4.6 0.3 1.0
CB A:PRO112 4.8 99.6 1.0
C03 A:GBQ1201 4.8 0.6 1.0
CD1 A:PHE264 4.8 0.7 1.0
C04 A:GBQ1201 5.0 0.4 1.0
CE2 A:PHE264 5.0 0.7 1.0

Fluorine binding site 4 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.5
occ:1.00
 F14 A:GBQ1201 0.0 0.5 1.0
C13 A:GBQ1201 1.3 0.1 1.0
F15 A:GBQ1201 2.1 0.5 1.0
F16 A:GBQ1201 2.1 0.9 1.0
C05 A:GBQ1201 2.3 0.4 1.0
C04 A:GBQ1201 2.8 0.4 1.0
C34 A:GBQ1201 3.2 1.0 1.0
F37 A:GBQ1201 3.4 0.3 1.0
C06 A:GBQ1201 3.4 0.2 1.0
C35 A:GBQ1201 3.5 0.4 1.0
C33 A:GBQ1201 3.7 0.6 1.0
CE2 A:PHE264 3.7 0.7 1.0
C36 A:GBQ1201 4.1 99.8 1.0
C03 A:GBQ1201 4.2 0.6 1.0
CE1 A:HIS265 4.2 0.1 1.0
C32 A:GBQ1201 4.3 99.8 1.0
CD2 A:PHE264 4.5 0.3 1.0
C31 A:GBQ1201 4.5 99.8 1.0
CZ A:PHE264 4.5 0.3 1.0
CG1 A:ILE113 4.5 94.5 1.0
C07 A:GBQ1201 4.6 0.6 1.0
CZ3 A:TRP261 4.6 0.0 1.0
CG2 A:ILE204 4.7 0.7 1.0
ND1 A:HIS265 4.8 0.5 1.0
C08 A:GBQ1201 4.8 0.8 1.0
O17 A:GBQ1201 5.0 0.4 1.0
CG1 A:VAL200 5.0 99.4 1.0

Fluorine binding site 5 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.5
occ:1.00
 F15 A:GBQ1201 0.0 0.5 1.0
C13 A:GBQ1201 1.3 0.1 1.0
F16 A:GBQ1201 2.1 0.9 1.0
F14 A:GBQ1201 2.1 0.5 1.0
C05 A:GBQ1201 2.2 0.4 1.0
C06 A:GBQ1201 2.6 0.2 1.0
CZ3 A:TRP261 3.2 0.0 1.0
CH2 A:TRP261 3.4 0.1 1.0
CG2 A:VAL116 3.4 91.3 1.0
C04 A:GBQ1201 3.5 0.4 1.0
CE3 A:TRP261 3.9 0.4 1.0
C07 A:GBQ1201 4.0 0.6 1.0
CB A:VAL116 4.0 90.7 1.0
CE2 A:PHE264 4.2 0.7 1.0
CZ2 A:TRP261 4.2 0.6 1.0
CG1 A:VAL116 4.3 88.7 1.0
O A:PRO112 4.5 97.7 1.0
F12 A:GBQ1201 4.6 0.7 1.0
C03 A:GBQ1201 4.7 0.6 1.0
CD2 A:PHE264 4.7 0.3 1.0
CD2 A:TRP261 4.7 0.5 1.0
CG2 A:ILE204 4.7 0.7 1.0
CZ A:PHE264 4.7 0.3 1.0
CE1 A:HIS265 4.7 0.1 1.0
CE2 A:TRP261 4.8 0.9 1.0
C08 A:GBQ1201 4.8 0.8 1.0
C A:PRO112 4.9 99.3 1.0
C09 A:GBQ1201 4.9 0.4 1.0

Fluorine binding site 6 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.9
occ:1.00
 F16 A:GBQ1201 0.0 0.9 1.0
C13 A:GBQ1201 1.3 0.1 1.0
F15 A:GBQ1201 2.1 0.5 1.0
F14 A:GBQ1201 2.1 0.5 1.0
C05 A:GBQ1201 2.2 0.4 1.0
C04 A:GBQ1201 2.9 0.4 1.0
C06 A:GBQ1201 3.3 0.2 1.0
CG1 A:ILE113 3.4 94.5 1.0
CA A:ILE113 3.4 93.1 1.0
N A:ILE113 3.5 94.9 1.0
O A:PRO112 3.6 97.7 1.0
C A:PRO112 3.6 99.3 1.0
CB A:ILE113 4.0 95.4 1.0
CG2 A:VAL116 4.0 91.3 1.0
C03 A:GBQ1201 4.2 0.6 1.0
CB A:VAL116 4.3 90.7 1.0
CB A:PRO112 4.3 99.6 1.0
C07 A:GBQ1201 4.5 0.6 1.0
C A:ILE113 4.6 98.5 1.0
CA A:PRO112 4.6 98.6 1.0
CD1 A:ILE113 4.6 0.0 1.0
CG2 A:ILE113 4.8 95.2 1.0
C08 A:GBQ1201 4.8 0.8 1.0
O A:ILE113 4.8 97.4 1.0
C33 A:GBQ1201 4.8 0.6 1.0
CG2 A:ILE204 4.9 0.7 1.0
C34 A:GBQ1201 4.9 1.0 1.0
F37 A:GBQ1201 4.9 0.3 1.0
CG1 A:VAL116 5.0 88.7 1.0

Fluorine binding site 7 out of 7 in 6j21

Go back to Fluorine Binding Sites List in 6j21
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:0.3
occ:1.00
 F37 A:GBQ1201 0.0 0.3 1.0
C34 A:GBQ1201 1.4 1.0 1.0
C33 A:GBQ1201 2.4 0.6 1.0
C35 A:GBQ1201 2.4 0.4 1.0
OG1 A:THR201 3.1 1.0 1.0
F14 A:GBQ1201 3.4 0.5 1.0
CG1 A:VAL200 3.5 99.4 1.0
C32 A:GBQ1201 3.7 99.8 1.0
C36 A:GBQ1201 3.7 99.8 1.0
CE1 A:HIS265 3.7 0.1 1.0
N A:THR201 3.8 96.5 1.0
ND1 A:HIS265 3.8 0.5 1.0
CA A:THR201 3.9 95.8 1.0
CB A:THR201 4.1 0.2 1.0
C31 A:GBQ1201 4.2 99.8 1.0
C A:VAL200 4.2 99.8 1.0
CB A:VAL200 4.2 99.5 1.0
O A:HIS197 4.3 95.8 1.0
CE1 A:HIS197 4.6 0.2 1.0
C13 A:GBQ1201 4.6 0.1 1.0
ND1 A:HIS197 4.7 1.0 1.0
O A:VAL200 4.8 99.4 1.0
CG2 A:ILE204 4.9 0.7 1.0
CA A:VAL200 4.9 95.8 1.0
F16 A:GBQ1201 4.9 0.9 1.0
CG2 A:THR201 5.0 96.2 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: Tue Jul 15 12:33:36 2025

Last articles

Mg in 5NOL
Mg in 5NOJ
Mg in 5NOG
Mg in 5NO9
Mg in 5NNW
Mg in 5NO1
Mg in 5NLM
Mg in 5NMX
Mg in 5NMW
Mg in 5NH7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy