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Fluorine in PDB 4ypq: Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid

Protein crystallography data

The structure of Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid, PDB code: 4ypq was solved by S.Leysen, M.Scheepstra, G.C.Van Almen, C.Ottmann, L.Brunsveld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.47 / 2.32
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 173.809, 173.809, 67.221, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 22.9

Other elements in 4ypq:

The structure of Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid (pdb code 4ypq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid, PDB code: 4ypq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4ypq

Go back to Fluorine Binding Sites List in 4ypq
Fluorine binding site 1 out of 3 in the Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid


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 Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:69.5
occ:1.00
F2 A:4F1601 0.0 69.5 1.0
C15 A:4F1601 1.2 44.5 1.0
F1 A:4F1601 1.9 41.3 1.0
F A:4F1601 2.0 54.6 1.0
C14 A:4F1601 2.3 50.4 1.0
C13 A:4F1601 2.7 41.8 1.0
C9 A:4F1601 3.5 42.3 1.0
CB A:GLN487 3.5 41.0 1.0
CG A:GLN487 3.7 34.8 1.0
CG A:GLN484 3.7 44.6 1.0
CE2 A:PHE506 3.7 53.1 1.0
O A:LEU505 3.8 49.7 1.0
CD2 A:PHE506 3.9 62.1 1.0
O A:LEU483 3.9 38.5 1.0
CA A:GLN484 4.0 38.0 1.0
C12 A:4F1601 4.0 40.3 1.0
C8 A:4F1601 4.1 40.0 1.0
CZ A:PHE506 4.1 52.6 1.0
C A:LEU483 4.3 40.3 1.0
N A:GLN484 4.3 42.9 1.0
CG A:PHE506 4.4 58.9 1.0
CB A:GLN484 4.4 43.0 1.0
O2 A:4F1601 4.5 35.7 1.0
O A:HOH721 4.5 52.6 1.0
CE1 A:PHE506 4.6 51.5 1.0
CD A:GLN487 4.6 44.2 1.0
C10 A:4F1601 4.6 59.9 1.0
CD1 A:PHE506 4.7 66.7 1.0
C A:LEU505 4.7 59.1 1.0
CA A:PHE506 4.8 65.6 1.0
C11 A:4F1601 4.8 51.5 1.0
CD A:GLN484 4.9 52.0 1.0
N1 A:4F1601 4.9 35.5 1.0
CB A:LEU483 4.9 30.6 1.0
OE1 A:GLN487 5.0 49.0 1.0

Fluorine binding site 2 out of 3 in 4ypq

Go back to Fluorine Binding Sites List in 4ypq
Fluorine binding site 2 out of 3 in the Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid


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 Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:41.3
occ:1.00
F1 A:4F1601 0.0 41.3 1.0
C15 A:4F1601 1.2 44.5 1.0
F2 A:4F1601 1.9 69.5 1.0
F A:4F1601 2.0 54.6 1.0
C14 A:4F1601 2.3 50.4 1.0
C8 A:4F1601 2.8 40.0 1.0
C9 A:4F1601 2.8 42.3 1.0
N1 A:4F1601 3.2 35.5 1.0
O2 A:4F1601 3.3 35.7 1.0
C13 A:4F1601 3.4 41.8 1.0
O A:LEU505 3.4 49.7 1.0
N A:4F1601 3.6 36.3 1.0
CZ A:PHE506 3.7 52.6 1.0
CE1 A:PHE506 3.8 51.5 1.0
CB A:LEU505 4.0 43.3 1.0
CE2 A:PHE506 4.0 53.1 1.0
CD1 A:PHE506 4.0 66.7 1.0
C A:LEU505 4.1 59.1 1.0
C16 A:4F1601 4.1 33.6 1.0
C10 A:4F1601 4.1 59.9 1.0
CG A:GLN484 4.1 44.6 1.0
CD2 A:PHE506 4.3 62.1 1.0
CG A:PHE506 4.3 58.9 1.0
C12 A:4F1601 4.5 40.3 1.0
C7 A:4F1601 4.5 39.3 1.0
NE2 A:GLN484 4.7 45.8 1.0
CA A:LEU505 4.7 53.7 1.0
C17 A:4F1601 4.7 36.8 1.0
N A:PHE506 4.8 64.1 1.0
C21 A:4F1601 4.8 35.1 1.0
C11 A:4F1601 4.8 51.5 1.0
CD A:GLN484 4.8 52.0 1.0
CA A:PHE506 4.8 65.6 1.0
CD2 A:LEU505 5.0 51.7 1.0

Fluorine binding site 3 out of 3 in 4ypq

Go back to Fluorine Binding Sites List in 4ypq
Fluorine binding site 3 out of 3 in the Crystal Structure of the Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid


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 Ror(Gamma)T Ligand Binding Domain in Complex with 4-(1-(2-Chloro-6-(Trifluoromethyl)Benzoyl)-1H-Indazol-3-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:54.6
occ:1.00
F A:4F1601 0.0 54.6 1.0
C15 A:4F1601 1.2 44.5 1.0
F1 A:4F1601 2.0 41.3 1.0
F2 A:4F1601 2.0 69.5 1.0
C14 A:4F1601 2.3 50.4 1.0
O2 A:4F1601 3.0 35.7 1.0
C9 A:4F1601 3.0 42.3 1.0
C8 A:4F1601 3.1 40.0 1.0
CG A:GLN484 3.2 44.6 1.0
C13 A:4F1601 3.3 41.8 1.0
N A:GLN484 3.6 42.9 1.0
CB A:LEU483 3.6 30.6 1.0
C A:LEU483 3.7 40.3 1.0
CA A:GLN484 3.7 38.0 1.0
O A:LEU483 3.8 38.5 1.0
O A:VAL480 3.9 46.4 1.0
CB A:GLN484 4.0 43.0 1.0
N1 A:4F1601 4.1 35.5 1.0
CD A:GLN484 4.1 52.0 1.0
CA A:LEU483 4.3 31.6 1.0
C10 A:4F1601 4.3 59.9 1.0
O A:LEU505 4.4 49.7 1.0
CG1 A:VAL480 4.5 28.1 1.0
NE2 A:GLN484 4.5 45.8 1.0
C12 A:4F1601 4.5 40.3 1.0
CD1 A:LEU483 4.5 30.9 1.0
CG A:LEU483 4.7 37.5 1.0
C A:VAL480 4.9 41.9 1.0
N A:4F1601 4.9 36.3 1.0
CB A:GLN487 4.9 41.0 1.0
C11 A:4F1601 4.9 51.5 1.0
C16 A:4F1601 4.9 33.6 1.0
OE1 A:GLN484 5.0 53.3 1.0

Reference:

M.Scheepstra, S.Leysen, G.C.Van Almen, J.R.Miller, J.Piesvaux, V.Kutilek, H.Van Eenennaam, H.Zhang, K.Barr, S.Nagpal, S.M.Soisson, M.Kornienko, K.Wiley, N.Elsen, S.Sharma, C.C.Correll, B.W.Trotter, M.Van Der Stelt, A.Oubrie, C.Ottmann, G.Parthasarathy, L.Brunsveld. Identification of An Allosteric Binding Site For Ror Gamma T Inhibition. Nat Commun V. 6 8833 2015.
ISSN: ESSN 2041-1723
PubMed: 26640126
DOI: 10.1038/NCOMMS9833
Page generated: Sun Dec 13 12:16:11 2020

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