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Fluorine in PDB 6vqf: Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist

Protein crystallography data

The structure of Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist, PDB code: 6vqf was solved by J.S.Sack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.507, 61.507, 157.911, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist (pdb code 6vqf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist, PDB code: 6vqf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6vqf

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Fluorine binding site 1 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.9
occ:1.00
 F15 A:R7V601 0.0 50.9 1.0
C14 A:R7V601 1.4 50.3 1.0
C35 A:R7V601 2.3 50.3 1.0
C42 A:R7V601 2.3 50.9 1.0
C6 A:R7V601 2.4 48.4 1.0
F45 A:R7V601 2.6 51.0 1.0
F37 A:R7V601 2.6 50.4 0.5
C5 A:R7V601 2.8 47.5 1.0
F36 A:R7V601 2.8 50.3 0.5
F44 A:R7V601 2.9 51.0 1.0
CD2 A:HIS479 3.4 36.8 1.0
F43 A:R7V601 3.5 51.4 1.0
F38 A:R7V601 3.5 50.1 0.5
C1 A:R7V601 3.6 47.9 1.0
CG A:HIS479 4.0 35.8 1.0
NE2 A:HIS479 4.0 36.8 1.0
CD2 A:LEU396 4.1 38.0 1.0
C4 A:R7V601 4.2 47.4 1.0
CD1 A:ILE400 4.2 38.4 1.0
CB A:HIS479 4.4 34.0 1.0
CE1 A:HIS479 4.7 37.0 1.0
C2 A:R7V601 4.7 47.7 1.0
CG A:LEU396 4.7 37.7 1.0
ND1 A:HIS479 4.7 37.0 1.0
CD2 A:LEU324 4.8 34.0 1.0
C3 A:R7V601 5.0 47.7 1.0

Fluorine binding site 2 out of 8 in 6vqf

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Fluorine binding site 2 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:49.8
occ:1.00
 F31 A:R7V601 0.0 49.8 1.0
C19 A:R7V601 1.4 49.7 1.0
C18 A:R7V601 2.3 49.6 1.0
C20 A:R7V601 2.3 49.8 1.0
CD1 A:ILE397 3.3 39.5 1.0
C17 A:R7V601 3.6 49.4 1.0
C21 A:R7V601 3.6 49.7 1.0
CE1 A:PHE401 3.7 35.5 1.0
CG2 A:ILE400 3.8 35.8 1.0
CD1 A:PHE401 4.1 34.9 1.0
C16 A:R7V601 4.1 49.6 1.0
CG2 A:ILE397 4.1 37.0 1.0
CD2 A:PHE388 4.2 37.3 1.0
CE2 A:PHE388 4.2 38.2 1.0
CD1 A:ILE400 4.2 38.4 1.0
CB A:ILE400 4.3 35.5 1.0
F45 A:R7V601 4.3 51.0 1.0
CA A:ILE397 4.4 36.0 1.0
CG A:PHE388 4.5 37.0 1.0
CG1 A:ILE397 4.5 38.0 1.0
CZ A:PHE388 4.5 38.3 1.0
CB A:ILE397 4.5 36.7 1.0
O A:ILE397 4.7 36.7 1.0
F43 A:R7V601 4.8 51.4 1.0
CD1 A:PHE388 4.8 38.0 1.0
CE1 A:PHE388 4.8 38.5 1.0
CZ A:PHE401 4.9 35.4 1.0
C10 A:R7V601 4.9 47.2 1.0
CG1 A:ILE400 4.9 36.9 1.0
C5 A:R7V601 4.9 47.5 1.0
C4 A:R7V601 5.0 47.4 1.0

Fluorine binding site 3 out of 8 in 6vqf

Go back to Fluorine Binding Sites List in 6vqf
Fluorine binding site 3 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.3
occ:0.50
 F36 A:R7V601 0.0 50.3 0.5
C35 A:R7V601 1.3 50.3 1.0
F37 A:R7V601 2.1 50.4 0.5
F38 A:R7V601 2.1 50.1 0.5
C14 A:R7V601 2.4 50.3 1.0
F15 A:R7V601 2.8 50.9 1.0
C6 A:R7V601 2.9 48.4 1.0
NE2 A:HIS479 3.0 36.8 1.0
C1 A:R7V601 3.0 47.9 1.0
CD2 A:LEU324 3.3 34.0 1.0
CD2 A:HIS479 3.5 36.8 1.0
OH A:TYR502 3.5 40.1 1.0
CE2 A:TYR502 3.7 38.2 1.0
C42 A:R7V601 3.8 50.9 1.0
CE1 A:HIS479 3.9 37.0 1.0
F44 A:R7V601 4.1 51.0 1.0
CZ A:TYR502 4.1 38.8 1.0
C5 A:R7V601 4.1 47.5 1.0
C2 A:R7V601 4.2 47.7 1.0
CB A:LEU324 4.3 33.2 1.0
F43 A:R7V601 4.3 51.4 1.0
CG A:LEU324 4.4 34.0 1.0
CG A:HIS479 4.5 35.8 1.0
ND1 A:HIS479 4.7 37.0 1.0
CA A:ALA321 4.7 33.2 1.0
O A:CYS320 4.8 36.0 1.0
F45 A:R7V601 4.8 51.0 1.0
C A:CYS320 4.8 35.3 1.0
CZ3 A:TRP317 4.8 34.7 1.0
N A:ALA321 4.8 34.4 1.0
CD2 A:TYR502 4.9 37.6 1.0

Fluorine binding site 4 out of 8 in 6vqf

Go back to Fluorine Binding Sites List in 6vqf
Fluorine binding site 4 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.4
occ:0.50
 F37 A:R7V601 0.0 50.4 0.5
C35 A:R7V601 1.3 50.3 1.0
F36 A:R7V601 2.1 50.3 0.5
F38 A:R7V601 2.1 50.1 0.5
C14 A:R7V601 2.4 50.3 1.0
F44 A:R7V601 2.6 51.0 1.0
F15 A:R7V601 2.6 50.9 1.0
CD2 A:HIS479 2.9 36.8 1.0
C42 A:R7V601 3.0 50.9 1.0
NE2 A:HIS479 3.1 36.8 1.0
CZ3 A:TRP317 3.4 34.7 1.0
OH A:TYR502 3.7 40.1 1.0
CH2 A:TRP317 3.7 35.0 1.0
C6 A:R7V601 3.7 48.4 1.0
F43 A:R7V601 3.8 51.4 1.0
F45 A:R7V601 4.0 51.0 1.0
CG A:HIS479 4.1 35.8 1.0
CE3 A:TRP317 4.2 33.7 1.0
C1 A:R7V601 4.3 47.9 1.0
CE1 A:HIS479 4.4 37.0 1.0
CD2 A:LEU396 4.5 38.0 1.0
CZ2 A:TRP317 4.7 35.1 1.0
CZ A:TYR502 4.8 38.8 1.0
C5 A:R7V601 4.9 47.5 1.0
ND1 A:HIS479 4.9 37.0 1.0
CB A:HIS479 5.0 34.0 1.0

Fluorine binding site 5 out of 8 in 6vqf

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Fluorine binding site 5 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:50.1
occ:0.50
 F38 A:R7V601 0.0 50.1 0.5
C35 A:R7V601 1.3 50.3 1.0
F37 A:R7V601 2.1 50.4 0.5
F36 A:R7V601 2.1 50.3 0.5
C14 A:R7V601 2.4 50.3 1.0
C42 A:R7V601 3.0 50.9 1.0
F43 A:R7V601 3.0 51.4 1.0
C1 A:R7V601 3.0 47.9 1.0
F44 A:R7V601 3.0 51.0 1.0
C6 A:R7V601 3.1 48.4 1.0
CB A:CYS320 3.5 36.0 1.0
F15 A:R7V601 3.5 50.9 1.0
CZ3 A:TRP317 4.0 34.7 1.0
CE3 A:TRP317 4.1 33.7 1.0
C A:CYS320 4.2 35.3 1.0
N A:ALA321 4.2 34.4 1.0
F45 A:R7V601 4.3 51.0 1.0
C2 A:R7V601 4.3 47.7 1.0
OH A:TYR502 4.4 40.1 1.0
CA A:CYS320 4.5 34.7 1.0
C5 A:R7V601 4.5 47.5 1.0
O A:CYS320 4.6 36.0 1.0
CH2 A:TRP317 4.6 35.0 1.0
NE2 A:HIS479 4.6 36.8 1.0
CA A:ALA321 4.7 33.2 1.0
CD2 A:HIS479 4.8 36.8 1.0
SG A:CYS320 4.8 42.1 1.0
CD2 A:TRP317 4.9 33.5 1.0
O A:TRP317 5.0 33.7 1.0

Fluorine binding site 6 out of 8 in 6vqf

Go back to Fluorine Binding Sites List in 6vqf
Fluorine binding site 6 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.4
occ:1.00
 F43 A:R7V601 0.0 51.4 1.0
C42 A:R7V601 1.3 50.9 1.0
F45 A:R7V601 2.1 51.0 1.0
F44 A:R7V601 2.1 51.0 1.0
C14 A:R7V601 2.4 50.3 1.0
C6 A:R7V601 2.8 48.4 1.0
F38 A:R7V601 3.0 50.1 0.5
C35 A:R7V601 3.2 50.3 1.0
CD1 A:LEU391 3.3 36.1 1.0
C1 A:R7V601 3.3 47.9 1.0
C18 A:R7V601 3.5 49.6 1.0
F15 A:R7V601 3.5 50.9 1.0
C5 A:R7V601 3.5 47.5 1.0
F37 A:R7V601 3.8 50.4 0.5
CD1 A:ILE397 3.9 39.5 1.0
C17 A:R7V601 3.9 49.4 1.0
CB A:CYS320 4.1 36.0 1.0
SG A:CYS320 4.3 42.1 1.0
C2 A:R7V601 4.3 47.7 1.0
F36 A:R7V601 4.3 50.3 0.5
C4 A:R7V601 4.5 47.4 1.0
C19 A:R7V601 4.5 49.7 1.0
CG A:LEU391 4.7 35.8 1.0
F31 A:R7V601 4.8 49.8 1.0
C3 A:R7V601 4.8 47.7 1.0
CD2 A:LEU391 4.9 34.9 1.0

Fluorine binding site 7 out of 8 in 6vqf

Go back to Fluorine Binding Sites List in 6vqf
Fluorine binding site 7 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


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 Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.0
occ:1.00
 F44 A:R7V601 0.0 51.0 1.0
C42 A:R7V601 1.3 50.9 1.0
F45 A:R7V601 2.1 51.0 1.0
F43 A:R7V601 2.1 51.4 1.0
C14 A:R7V601 2.4 50.3 1.0
F37 A:R7V601 2.6 50.4 0.5
C35 A:R7V601 2.8 50.3 1.0
F15 A:R7V601 2.9 50.9 1.0
F38 A:R7V601 3.0 50.1 0.5
CD2 A:LEU396 3.6 38.0 1.0
C6 A:R7V601 3.7 48.4 1.0
SG A:CYS393 3.8 45.1 1.0
CD1 A:LEU391 4.0 36.1 1.0
F36 A:R7V601 4.1 50.3 0.5
CH2 A:TRP317 4.3 35.0 1.0
CG A:LEU396 4.4 37.7 1.0
C5 A:R7V601 4.5 47.5 1.0
CD1 A:ILE397 4.5 39.5 1.0
C1 A:R7V601 4.5 47.9 1.0
CZ3 A:TRP317 4.6 34.7 1.0
CZ2 A:TRP317 4.7 35.1 1.0
CD2 A:HIS479 4.8 36.8 1.0

Fluorine binding site 8 out of 8 in 6vqf

Go back to Fluorine Binding Sites List in 6vqf
Fluorine binding site 8 out of 8 in the Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692)) in Complex with An Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.0
occ:1.00
 F45 A:R7V601 0.0 51.0 1.0
C42 A:R7V601 1.3 50.9 1.0
F44 A:R7V601 2.1 51.0 1.0
F43 A:R7V601 2.1 51.4 1.0
C14 A:R7V601 2.4 50.3 1.0
F15 A:R7V601 2.6 50.9 1.0
C6 A:R7V601 3.1 48.4 1.0
C5 A:R7V601 3.2 47.5 1.0
CD1 A:ILE400 3.2 38.4 1.0
CD1 A:ILE397 3.6 39.5 1.0
C35 A:R7V601 3.7 50.3 1.0
CD2 A:LEU396 3.9 38.0 1.0
CG A:LEU396 4.0 37.7 1.0
F37 A:R7V601 4.0 50.4 0.5
C18 A:R7V601 4.0 49.6 1.0
C1 A:R7V601 4.2 47.9 1.0
F38 A:R7V601 4.3 50.1 0.5
F31 A:R7V601 4.3 49.8 1.0
C4 A:R7V601 4.4 47.4 1.0
C19 A:R7V601 4.6 49.7 1.0
CG1 A:ILE400 4.6 36.9 1.0
CD1 A:LEU391 4.7 36.1 1.0
CG1 A:ILE397 4.8 38.0 1.0
F36 A:R7V601 4.8 50.3 0.5
C17 A:R7V601 4.8 49.4 1.0
CD1 A:LEU396 4.9 38.7 1.0
SG A:CYS393 4.9 45.1 1.0

Reference:

R.J.Cherney, L.A.M.Cornelius, A.Srivastana, C.A.Weigelt, D.Marcoux, J.J.W.Duan, Q.Shi, D.G.Batt, Q.Liu, S.Yip, D.R.Wu, M.Ruzanov, J.S.Sack, J.Wang, M.Yarde, M.E.Cvijic, A.Mathur, S.Li, D.Shuster, V.Borowski, J.Xie, K.W.Mcintyre, M.Obermeier, A.Fura, K.Stefanski, G.Cornelius, J.A.Tino, J.E.Macor, L.Salter-Cid, R.Denton, Q.Zhao, P.H.Carter, T.G.M.Dhar. Discovery of Bms-986251: A Clinically Viable, Potent and Selective Rorgt Inverse Agonist Acs Med.Chem.Lett. 2020.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.0C00063
Page generated: Tue Jul 15 16:46:58 2025

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