Atomistry » Fluorine » PDB 3ohh-3oyj » 3ook
Atomistry »
  Fluorine »
    PDB 3ohh-3oyj »
      3ook »

Fluorine in PDB 3ook: Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid

Protein crystallography data

The structure of Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid, PDB code: 3ook was solved by M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.14 / 2.29
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.477, 83.288, 190.007, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.1

Other elements in 3ook:

The structure of Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid (pdb code 3ook). 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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid, PDB code: 3ook:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic 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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:36.2
occ:1.00
F26 A:OOK1 0.0 36.2 1.0
C12 A:OOK1 1.3 34.1 1.0
C19 A:OOK1 2.3 30.5 1.0
C8 A:OOK1 2.4 33.5 1.0
N7 A:OOK1 2.8 32.2 1.0
C10 A:OOK1 3.2 33.0 1.0
C6 A:OOK1 3.5 29.6 1.0
C16 A:OOK1 3.5 34.0 1.0
CD1 A:ILE339 3.6 39.0 1.0
C13 A:OOK1 3.6 33.4 1.0
C4 A:OOK1 3.7 29.0 1.0
C11 A:OOK1 3.7 34.1 1.0
OG A:SER336 3.7 22.8 1.0
CA A:SER336 3.8 23.9 1.0
O21 A:OOK1 3.8 29.9 1.0
CG2 A:ILE273 3.8 50.9 1.0
F28 A:OOK1 3.8 37.3 1.0
C20 A:OOK1 4.1 33.3 1.0
CB A:SER336 4.2 22.5 1.0
CB A:ILE339 4.2 34.4 1.0
N1 A:OOK1 4.2 29.3 1.0
C18 A:OOK1 4.2 31.6 1.0
CG2 A:ILE339 4.4 34.8 1.0
N A:SER336 4.4 23.9 1.0
C5 A:OOK1 4.4 24.1 1.0
CG1 A:ILE339 4.5 33.4 1.0
C9 A:OOK1 4.5 29.3 1.0
CE A:MET294 4.6 32.8 1.0
O A:ARG335 4.6 26.6 1.0
C14 A:OOK1 4.7 26.6 1.0
CD1 A:ILE273 4.7 56.6 1.0
C A:ARG335 4.8 26.3 1.0
O A:SER336 4.8 28.5 1.0
F27 A:OOK1 4.8 35.9 1.0
C A:SER336 4.8 29.9 1.0
C15 A:OOK1 4.8 34.8 1.0
CB A:ILE273 4.9 52.9 1.0

Fluorine binding site 2 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 2 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic 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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:35.9
occ:1.00
F27 A:OOK1 0.0 35.9 1.0
C11 A:OOK1 1.4 34.1 1.0
C20 A:OOK1 2.4 33.3 1.0
C8 A:OOK1 2.4 33.5 1.0
N7 A:OOK1 2.8 32.2 1.0
C6 A:OOK1 3.4 29.6 1.0
SD A:MET332 3.5 41.7 1.0
O21 A:OOK1 3.5 29.9 1.0
CG A:MET332 3.6 35.7 1.0
CB A:MET294 3.6 28.1 1.0
C13 A:OOK1 3.7 33.4 1.0
N A:ALA295 3.7 25.9 1.0
C12 A:OOK1 3.7 34.1 1.0
C A:MET294 3.7 28.9 1.0
CA A:ALA295 3.9 25.7 1.0
O A:MET294 3.9 29.9 1.0
C19 A:OOK1 4.2 30.5 1.0
CB A:ALA295 4.3 26.0 1.0
CA A:MET294 4.3 25.6 1.0
C9 A:OOK1 4.5 29.3 1.0
CB A:HIS298 4.6 24.5 1.0
CE A:MET294 4.7 32.8 1.0
OG A:SER336 4.7 22.8 1.0
O A:LEU291 4.7 26.5 1.0
CD1 A:LEU291 4.7 26.6 1.0
F26 A:OOK1 4.8 36.2 1.0
CG A:MET294 4.9 31.9 1.0
C24 A:OOK1 4.9 31.5 1.0
C15 A:OOK1 4.9 34.8 1.0
CE A:MET332 4.9 39.4 1.0

Fluorine binding site 3 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic 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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:37.3
occ:1.00
F28 A:OOK1 0.0 37.3 1.0
C16 A:OOK1 1.3 34.0 1.0
C10 A:OOK1 2.3 33.0 1.0
C18 A:OOK1 2.4 31.6 1.0
F29 A:OOK1 2.7 33.8 1.0
CG2 A:ILE339 3.4 34.8 1.0
CG2 A:ILE273 3.4 50.9 1.0
C4 A:OOK1 3.6 29.0 1.0
C14 A:OOK1 3.6 26.6 1.0
CD1 A:ILE277 3.7 44.2 1.0
CG2 A:THR274 3.8 43.0 1.0
F26 A:OOK1 3.8 36.2 1.0
CD1 A:LEU352 4.0 51.6 1.0
C5 A:OOK1 4.1 24.1 1.0
CB A:ILE339 4.3 34.4 1.0
CD1 A:ILE356 4.5 23.1 1.0
CB A:ILE273 4.6 52.9 1.0
CD2 A:LEU352 4.6 52.5 1.0
CG A:LEU352 4.8 51.1 1.0
N A:THR274 4.8 44.9 1.0
N1 A:OOK1 4.9 29.3 1.0
C A:ILE339 4.9 38.7 1.0
CA A:THR274 4.9 44.9 1.0
C A:ILE273 4.9 49.9 1.0
CB A:THR274 5.0 48.9 1.0

Fluorine binding site 4 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid


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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:33.8
occ:1.00
F29 A:OOK1 0.0 33.8 1.0
C18 A:OOK1 1.3 31.6 1.0
C14 A:OOK1 2.3 26.6 1.0
C16 A:OOK1 2.4 34.0 1.0
F28 A:OOK1 2.7 37.3 1.0
CA A:PHE340 3.1 36.4 1.0
N A:PHE340 3.2 35.5 1.0
CB A:PHE340 3.3 38.1 1.0
CD1 A:PHE340 3.6 45.0 1.0
O A:SER336 3.6 28.5 1.0
C5 A:OOK1 3.6 24.1 1.0
C10 A:OOK1 3.6 33.0 1.0
C A:ILE339 3.8 38.7 1.0
CD1 A:ILE356 3.8 23.1 1.0
CD2 A:LEU352 3.8 52.5 1.0
CG A:PHE340 3.9 40.6 1.0
C4 A:OOK1 4.1 29.0 1.0
O A:ILE339 4.1 40.4 1.0
CG2 A:ILE339 4.1 34.8 1.0
CG A:LEU352 4.3 51.1 1.0
CD1 A:LEU352 4.4 51.6 1.0
CB A:ILE339 4.5 34.4 1.0
C A:PHE340 4.5 43.6 1.0
C A:SER336 4.6 29.9 1.0
CA A:ILE339 4.7 32.2 1.0
CE1 A:PHE340 4.8 46.4 1.0
N3 A:OOK1 4.8 25.0 1.0
CG2 A:THR274 5.0 43.0 1.0
O A:PHE340 5.0 41.4 1.0

Fluorine binding site 5 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid


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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2

b:40.0
occ:1.00
F26 C:OOK2 0.0 40.0 1.0
C12 C:OOK2 1.3 39.6 1.0
C19 C:OOK2 2.3 40.5 1.0
C8 C:OOK2 2.4 40.2 1.0
N7 C:OOK2 2.8 42.0 1.0
C10 C:OOK2 3.3 27.5 1.0
OG C:SER336 3.4 25.1 1.0
C6 C:OOK2 3.4 39.9 1.0
CD1 C:ILE339 3.4 47.0 1.0
CA C:SER336 3.5 26.0 1.0
C13 C:OOK2 3.6 39.0 1.0
C16 C:OOK2 3.6 29.4 1.0
C11 C:OOK2 3.7 37.5 1.0
O21 C:OOK2 3.7 38.1 1.0
C4 C:OOK2 3.7 26.6 1.0
CB C:SER336 3.8 24.4 1.0
CG2 C:ILE273 3.8 59.2 1.0
F28 C:OOK2 4.0 34.4 1.0
C20 C:OOK2 4.1 37.0 1.0
N C:SER336 4.1 27.3 1.0
CB C:ILE339 4.2 41.6 1.0
N1 C:OOK2 4.2 32.1 1.0
C18 C:OOK2 4.3 29.9 1.0
CG1 C:ILE339 4.4 42.3 1.0
C5 C:OOK2 4.4 26.5 1.0
CG2 C:ILE339 4.5 42.7 1.0
C9 C:OOK2 4.5 38.2 1.0
O C:ARG335 4.6 29.0 1.0
C C:SER336 4.6 30.3 1.0
O C:SER336 4.6 31.1 1.0
C C:ARG335 4.6 30.2 1.0
C14 C:OOK2 4.6 27.2 1.0
CE C:MET294 4.8 44.8 1.0
F27 C:OOK2 4.8 36.2 1.0
C15 C:OOK2 4.8 39.7 1.0
CD1 C:ILE273 4.8 66.5 1.0
CB C:ILE273 4.9 58.7 1.0

Fluorine binding site 6 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid


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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2

b:36.2
occ:1.00
F27 C:OOK2 0.0 36.2 1.0
C11 C:OOK2 1.3 37.5 1.0
C20 C:OOK2 2.4 37.0 1.0
C8 C:OOK2 2.4 40.2 1.0
N7 C:OOK2 2.8 42.0 1.0
C6 C:OOK2 3.4 39.9 1.0
CB C:MET294 3.5 38.5 1.0
O21 C:OOK2 3.6 38.1 1.0
C13 C:OOK2 3.6 39.0 1.0
C12 C:OOK2 3.6 39.6 1.0
N C:ALA295 3.7 32.2 1.0
CG C:MET332 3.7 42.9 1.0
C C:MET294 3.8 36.9 1.0
SD C:MET332 3.9 48.9 1.0
CA C:ALA295 3.9 30.9 1.0
O C:MET294 4.1 35.2 1.0
C19 C:OOK2 4.1 40.5 1.0
CB C:ALA295 4.2 31.0 1.0
CA C:MET294 4.3 35.8 1.0
CD1 C:LEU291 4.3 33.5 1.0
O C:LEU291 4.5 36.4 1.0
C9 C:OOK2 4.5 38.2 1.0
CE C:MET294 4.6 44.8 1.0
OG C:SER336 4.7 25.1 1.0
CG C:MET294 4.7 42.7 1.0
F26 C:OOK2 4.8 40.0 1.0
C15 C:OOK2 4.9 39.7 1.0
CB C:HIS298 4.9 27.1 1.0
C24 C:OOK2 5.0 37.4 1.0
O C:HOH30 5.0 34.9 1.0

Fluorine binding site 7 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid


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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2

b:34.4
occ:1.00
F28 C:OOK2 0.0 34.4 1.0
C16 C:OOK2 1.3 29.4 1.0
C10 C:OOK2 2.4 27.5 1.0
C18 C:OOK2 2.4 29.9 1.0
F29 C:OOK2 2.7 37.5 1.0
CG2 C:ILE339 3.4 42.7 1.0
CG2 C:ILE273 3.4 59.2 1.0
CD1 C:ILE277 3.5 57.0 1.0
C4 C:OOK2 3.6 26.6 1.0
C14 C:OOK2 3.6 27.2 1.0
CG2 C:THR274 3.9 47.0 1.0
F26 C:OOK2 4.0 40.0 1.0
CD1 C:LEU352 4.0 38.8 1.0
C5 C:OOK2 4.1 26.5 1.0
CD1 C:ILE356 4.3 47.2 1.0
CB C:ILE339 4.3 41.6 1.0
CB C:ILE273 4.6 58.7 1.0
CD2 C:LEU352 4.7 42.8 1.0
N C:THR274 4.7 48.6 1.0
C C:ILE273 4.8 54.7 1.0
CG C:LEU352 4.8 40.6 1.0
CA C:THR274 4.8 48.0 1.0
N1 C:OOK2 4.9 32.1 1.0
CG1 C:ILE277 5.0 55.5 1.0

Fluorine binding site 8 out of 8 in 3ook

Go back to Fluorine Binding Sites List in 3ook
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid


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 Human Fxr in Complex with 4-({(2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2- Cyclohexylacetyl}Amino)-3,5-Difluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2

b:37.5
occ:1.00
F29 C:OOK2 0.0 37.5 1.0
C18 C:OOK2 1.3 29.9 1.0
C16 C:OOK2 2.3 29.4 1.0
C14 C:OOK2 2.3 27.2 1.0
F28 C:OOK2 2.7 34.4 1.0
CA C:PHE340 3.1 40.8 1.0
N C:PHE340 3.1 39.8 1.0
CB C:PHE340 3.3 43.0 1.0
O C:SER336 3.5 31.1 1.0
C10 C:OOK2 3.6 27.5 1.0
C5 C:OOK2 3.6 26.5 1.0
CD1 C:PHE340 3.8 49.5 1.0
CD2 C:LEU352 3.8 42.8 1.0
C C:ILE339 3.8 42.6 1.0
CD1 C:ILE356 3.8 47.2 1.0
CG2 C:ILE339 4.0 42.7 1.0
CG C:PHE340 4.0 45.6 1.0
C4 C:OOK2 4.1 26.6 1.0
CG C:LEU352 4.3 40.6 1.0
CB C:ILE339 4.3 41.6 1.0
O C:ILE339 4.4 42.8 1.0
CD1 C:LEU352 4.4 38.8 1.0
C C:PHE340 4.6 46.1 1.0
CA C:ILE339 4.6 37.5 1.0
C C:SER336 4.6 30.3 1.0
N3 C:OOK2 4.9 30.8 1.0
CG2 C:THR274 5.0 47.0 1.0

Reference:

H.G.F.Richter, G.M.Benson, K.H.Bleicher, D.Blum, E.Chaput, N.Clemann, S.Feng, C.Gardes, U.Grether, P.Hartman, B.Kuhn, R.E.Martin, J.M.Plancher, M.G.Rudolph, F.Schuler, S.Taylor. Optimization of A Novel Class of Benzimidazole-Based Farnesoid X Receptor (Fxr) Agonists to Improve Physicochemical and Adme Properties Bioorg.Med.Chem.Lett. V. 21 1134 2011.
ISSN: ISSN 0960-894X
PubMed: 21269824
DOI: 10.1016/J.BMCL.2010.12.123
Page generated: Sun Dec 13 11:52:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy