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Fluorine in PDB 7kqj: Crystal Structure of Rar-Related Orphan Receptor C (Nhis-Rorgt(244- 487)-L6-SRC1(678-692) in Complex with A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist, PDB code: 7kqj 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) 59.27 / 2.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.809, 63.809, 159.923, 90, 90, 90
R / Rfree (%) 20.6 / 25.4

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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist (pdb code 7kqj). 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist, PDB code: 7kqj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7kqj

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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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:93.1
occ:1.00
 F16 A:Z8G4000 0.0 93.1 1.0
C15 A:Z8G4000 1.4 93.2 1.0
C34 A:Z8G4000 2.3 92.8 1.0
C33 A:Z8G4000 2.3 94.2 1.0
C1 A:Z8G4000 2.4 92.7 1.0
H43 A:Z8G4000 2.5 110.7 0.0
F38 A:Z8G4000 2.6 93.0 1.0
F37 A:Z8G4000 2.6 94.5 1.0
F39 A:Z8G4000 2.8 92.6 1.0
C6 A:Z8G4000 2.8 92.2 1.0
F35 A:Z8G4000 2.8 94.5 1.0
CD2 A:HIS479 3.1 56.9 1.0
F40 A:Z8G4000 3.5 92.6 1.0
F36 A:Z8G4000 3.5 94.1 1.0
C2 A:Z8G4000 3.6 92.5 1.0
CG A:HIS479 3.8 56.0 1.0
NE2 A:HIS479 3.9 57.6 1.0
H41 A:Z8G4000 4.0 111.0 0.0
C5 A:Z8G4000 4.2 92.1 1.0
CD2 A:LEU396 4.2 51.1 1.0
CE A:MET358 4.2 59.4 1.0
CB A:HIS479 4.3 54.4 1.0
CD1 A:ILE400 4.3 52.1 1.0
H47 A:Z8G4000 4.7 110.1 0.0
C3 A:Z8G4000 4.7 92.5 1.0
CE1 A:HIS479 4.8 57.8 1.0
CG A:LEU396 4.8 50.8 1.0
ND1 A:HIS479 4.8 57.6 1.0
CA A:HIS479 5.0 53.9 1.0
CD2 A:LEU324 5.0 48.1 1.0
C4 A:Z8G4000 5.0 92.6 1.0

Fluorine binding site 2 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:94.6
occ:1.00
 F32 A:Z8G4000 0.0 94.6 1.0
C22 A:Z8G4000 1.4 94.4 1.0
C23 A:Z8G4000 2.3 94.4 1.0
C21 A:Z8G4000 2.3 94.2 1.0
H56 A:Z8G4000 2.6 113.2 0.0
H55 A:Z8G4000 2.6 113.1 0.0
CE1 A:PHE401 3.0 51.1 1.0
CD1 A:PHE401 3.3 50.5 1.0
CG2 A:ILE400 3.5 49.9 1.0
CG2 A:ILE397 3.5 49.6 1.0
C20 A:Z8G4000 3.6 94.3 1.0
C24 A:Z8G4000 3.6 94.4 1.0
CD1 A:ILE397 3.7 51.9 1.0
CB A:ILE400 4.0 49.4 1.0
O A:ILE397 4.1 50.6 1.0
C19 A:Z8G4000 4.1 94.6 1.0
CA A:ILE397 4.1 49.5 1.0
CD2 A:PHE388 4.1 47.1 1.0
CZ A:PHE401 4.2 50.9 1.0
CD1 A:ILE400 4.2 52.1 1.0
CB A:ILE397 4.2 49.4 1.0
CE2 A:PHE388 4.3 47.6 1.0
H57 A:Z8G4000 4.5 113.3 0.0
H54 A:Z8G4000 4.5 113.2 0.0
H48 A:Z8G4000 4.5 110.1 0.0
C A:ILE397 4.5 50.0 1.0
CG1 A:ILE397 4.5 50.4 1.0
CG A:PHE388 4.6 46.5 1.0
CG A:PHE401 4.7 49.8 1.0
CG1 A:ILE400 4.8 50.5 1.0
CZ A:PHE388 4.9 47.5 1.0
N A:PHE401 5.0 48.6 1.0

Fluorine binding site 3 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:94.5
occ:1.00
 F35 A:Z8G4000 0.0 94.5 1.0
C33 A:Z8G4000 1.3 94.2 1.0
F37 A:Z8G4000 2.1 94.5 1.0
F36 A:Z8G4000 2.1 94.1 1.0
C15 A:Z8G4000 2.4 93.2 1.0
H41 A:Z8G4000 2.8 111.0 0.0
F16 A:Z8G4000 2.8 93.1 1.0
C1 A:Z8G4000 2.9 92.7 1.0
C2 A:Z8G4000 3.0 92.5 1.0
NE2 A:HIS479 3.3 57.6 1.0
CD2 A:LEU324 3.3 48.1 1.0
CD2 A:HIS479 3.6 56.9 1.0
OH A:TYR502 3.6 60.5 1.0
C34 A:Z8G4000 3.7 92.8 1.0
CE2 A:TYR502 3.8 58.7 1.0
C6 A:Z8G4000 4.0 92.2 1.0
F39 A:Z8G4000 4.1 92.6 1.0
CZ A:TYR502 4.2 59.4 1.0
CG A:LEU324 4.2 47.1 1.0
C3 A:Z8G4000 4.2 92.5 1.0
CB A:LEU324 4.2 45.9 1.0
F40 A:Z8G4000 4.3 92.6 1.0
CD1 A:LEU324 4.4 47.3 1.0
CE1 A:HIS479 4.4 57.8 1.0
H43 A:Z8G4000 4.4 110.7 0.0
O A:CYS320 4.5 46.8 1.0
H42 A:Z8G4000 4.7 111.0 0.0
CG A:HIS479 4.7 56.0 1.0
F38 A:Z8G4000 4.7 93.0 1.0
C A:CYS320 4.9 46.4 1.0
CA A:ALA321 4.9 46.2 1.0
C5 A:Z8G4000 4.9 92.1 1.0
CD2 A:TYR502 4.9 57.7 1.0
CZ3 A:TRP317 5.0 51.6 1.0

Fluorine binding site 4 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:94.1
occ:1.00
 F36 A:Z8G4000 0.0 94.1 1.0
C33 A:Z8G4000 1.3 94.2 1.0
H41 A:Z8G4000 2.1 111.0 0.0
F35 A:Z8G4000 2.1 94.5 1.0
F37 A:Z8G4000 2.2 94.5 1.0
C15 A:Z8G4000 2.4 93.2 1.0
C2 A:Z8G4000 2.9 92.5 1.0
F40 A:Z8G4000 2.9 92.6 1.0
C34 A:Z8G4000 2.9 92.8 1.0
C1 A:Z8G4000 3.0 92.7 1.0
F39 A:Z8G4000 3.2 92.6 1.0
F16 A:Z8G4000 3.5 93.1 1.0
CB A:CYS320 3.5 46.0 1.0
C3 A:Z8G4000 4.2 92.5 1.0
CZ3 A:TRP317 4.2 51.6 1.0
CE3 A:TRP317 4.2 50.8 1.0
C A:CYS320 4.2 46.4 1.0
F38 A:Z8G4000 4.2 93.0 1.0
O A:CYS320 4.3 46.8 1.0
N A:ALA321 4.4 46.1 1.0
C6 A:Z8G4000 4.4 92.2 1.0
OH A:TYR502 4.4 60.5 1.0
CA A:CYS320 4.5 46.0 1.0
H42 A:Z8G4000 4.5 111.0 0.0
O A:TRP317 4.7 50.6 1.0
SG A:CYS320 4.8 48.0 1.0
CH2 A:TRP317 4.9 51.8 1.0
CA A:ALA321 4.9 46.2 1.0
CD2 A:TRP317 4.9 50.1 1.0
CD2 A:HIS479 4.9 56.9 1.0
H43 A:Z8G4000 5.0 110.7 0.0
NE2 A:HIS479 5.0 57.6 1.0
CE2 A:TYR502 5.0 58.7 1.0

Fluorine binding site 5 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:94.5
occ:1.00
 F37 A:Z8G4000 0.0 94.5 1.0
C33 A:Z8G4000 1.3 94.2 1.0
F35 A:Z8G4000 2.1 94.5 1.0
F36 A:Z8G4000 2.2 94.1 1.0
C15 A:Z8G4000 2.4 93.2 1.0
F39 A:Z8G4000 2.6 92.6 1.0
F16 A:Z8G4000 2.6 93.1 1.0
C34 A:Z8G4000 3.0 92.8 1.0
CD2 A:HIS479 3.0 56.9 1.0
CZ3 A:TRP317 3.3 51.6 1.0
NE2 A:HIS479 3.4 57.6 1.0
OH A:TYR502 3.5 60.5 1.0
C1 A:Z8G4000 3.7 92.7 1.0
F40 A:Z8G4000 3.7 92.6 1.0
CH2 A:TRP317 3.7 51.8 1.0
H41 A:Z8G4000 3.9 111.0 0.0
CE3 A:TRP317 4.0 50.8 1.0
F38 A:Z8G4000 4.1 93.0 1.0
C2 A:Z8G4000 4.2 92.5 1.0
CG A:HIS479 4.3 56.0 1.0
CZ A:TYR502 4.7 59.4 1.0
CE1 A:HIS479 4.7 57.8 1.0
CZ2 A:TRP317 4.7 51.6 1.0
C6 A:Z8G4000 4.8 92.2 1.0
CE2 A:TYR502 4.9 58.7 1.0
CD2 A:LEU396 4.9 51.1 1.0
H43 A:Z8G4000 4.9 110.7 0.0
CD2 A:TRP317 5.0 50.1 1.0

Fluorine binding site 6 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:93.0
occ:1.00
 F38 A:Z8G4000 0.0 93.0 1.0
C34 A:Z8G4000 1.3 92.8 1.0
F40 A:Z8G4000 2.1 92.6 1.0
F39 A:Z8G4000 2.1 92.6 1.0
C15 A:Z8G4000 2.4 93.2 1.0
F16 A:Z8G4000 2.6 93.1 1.0
H43 A:Z8G4000 2.9 110.7 0.0
C1 A:Z8G4000 3.0 92.7 1.0
CD1 A:ILE400 3.1 52.1 1.0
C6 A:Z8G4000 3.2 92.2 1.0
H55 A:Z8G4000 3.5 113.1 0.0
C33 A:Z8G4000 3.7 94.2 1.0
CD2 A:LEU396 3.7 51.1 1.0
CD1 A:ILE397 3.8 51.9 1.0
CG A:LEU396 3.9 50.8 1.0
C2 A:Z8G4000 4.1 92.5 1.0
F37 A:Z8G4000 4.1 94.5 1.0
C21 A:Z8G4000 4.1 94.2 1.0
F36 A:Z8G4000 4.2 94.1 1.0
C5 A:Z8G4000 4.3 92.1 1.0
H54 A:Z8G4000 4.5 113.2 0.0
H41 A:Z8G4000 4.5 111.0 0.0
CD1 A:LEU396 4.6 51.0 1.0
CG1 A:ILE400 4.6 50.5 1.0
C20 A:Z8G4000 4.6 94.3 1.0
F35 A:Z8G4000 4.7 94.5 1.0
C22 A:Z8G4000 4.9 94.4 1.0
H47 A:Z8G4000 5.0 110.1 0.0
SG A:CYS393 5.0 59.6 1.0

Fluorine binding site 7 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:92.6
occ:1.00
 F39 A:Z8G4000 0.0 92.6 1.0
C34 A:Z8G4000 1.3 92.8 1.0
F40 A:Z8G4000 2.1 92.6 1.0
F38 A:Z8G4000 2.1 93.0 1.0
C15 A:Z8G4000 2.4 93.2 1.0
F37 A:Z8G4000 2.6 94.5 1.0
F16 A:Z8G4000 2.8 93.1 1.0
C33 A:Z8G4000 2.8 94.2 1.0
F36 A:Z8G4000 3.2 94.1 1.0
CD2 A:LEU396 3.5 51.1 1.0
C1 A:Z8G4000 3.7 92.7 1.0
SG A:CYS393 4.0 59.6 1.0
F35 A:Z8G4000 4.1 94.5 1.0
CH2 A:TRP317 4.2 51.8 1.0
CG A:LEU396 4.3 50.8 1.0
H43 A:Z8G4000 4.4 110.7 0.0
H41 A:Z8G4000 4.5 111.0 0.0
CZ3 A:TRP317 4.5 51.6 1.0
C2 A:Z8G4000 4.5 92.5 1.0
CD1 A:LEU391 4.5 42.0 1.0
C6 A:Z8G4000 4.5 92.2 1.0
CZ2 A:TRP317 4.5 51.6 1.0
CD2 A:HIS479 4.7 56.9 1.0
CD1 A:ILE397 4.7 51.9 1.0

Fluorine binding site 8 out of 8 in 7kqj

Go back to Fluorine Binding Sites List in 7kqj
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 A Novel Tricyclic-Carbocylic Rorgt 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 A Novel Tricyclic-Carbocylic Rorgt Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:92.6
occ:1.00
 F40 A:Z8G4000 0.0 92.6 1.0
C34 A:Z8G4000 1.3 92.8 1.0
F38 A:Z8G4000 2.1 93.0 1.0
F39 A:Z8G4000 2.1 92.6 1.0
C15 A:Z8G4000 2.4 93.2 1.0
C1 A:Z8G4000 2.8 92.7 1.0
F36 A:Z8G4000 2.9 94.1 1.0
C33 A:Z8G4000 3.1 94.2 1.0
C2 A:Z8G4000 3.2 92.5 1.0
H41 A:Z8G4000 3.2 111.0 0.0
H55 A:Z8G4000 3.3 113.1 0.0
CD1 A:LEU391 3.4 42.0 1.0
F16 A:Z8G4000 3.5 93.1 1.0
H54 A:Z8G4000 3.6 113.2 0.0
C6 A:Z8G4000 3.7 92.2 1.0
F37 A:Z8G4000 3.7 94.5 1.0
H43 A:Z8G4000 4.0 110.7 0.0
C21 A:Z8G4000 4.1 94.2 1.0
CD1 A:ILE397 4.1 51.9 1.0
C20 A:Z8G4000 4.2 94.3 1.0
C3 A:Z8G4000 4.2 92.5 1.0
F35 A:Z8G4000 4.3 94.5 1.0
CB A:CYS320 4.3 46.0 1.0
SG A:CYS320 4.4 48.0 1.0
C5 A:Z8G4000 4.6 92.1 1.0
CG A:LEU391 4.7 42.2 1.0
H42 A:Z8G4000 4.9 111.0 0.0
C4 A:Z8G4000 4.9 92.6 1.0
CD2 A:LEU391 4.9 42.5 1.0

Reference:

M.G.Yang, M.Beaudoin-Bertrand, Z.Xiao, D.Marcoux, C.A.Weigelt, S.Yip, D.R.Wu, M.Ruzanov, J.S.Sack, J.Wang, M.Yarde, S.Li, D.J.Shuster, J.H.Xie, T.Sherry, M.T.Obermeier, A.Fura, K.Stefanski, G.Cornelius, P.Khandelwal, A.Karmakar, M.Basha, V.Babu, A.K.Gupta, A.Mathur, L.Salter-Cid, R.Denton, Q.Zhao, T.G.M.Dhar. Tricyclic-Carbocyclic Ror Gamma T Inverse Agonists-Discovery of Bms-986313. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33591748
DOI: 10.1021/ACS.JMEDCHEM.0C01992
Page generated: Fri Aug 2 08:27:14 2024

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