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Chlorine in PDB 3omk: Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide

Protein crystallography data

The structure of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide, PDB code: 3omk 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) 38.68 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.320, 84.710, 190.010, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.5

Other elements in 3omk:

The structure of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide (pdb code 3omk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide, PDB code: 3omk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3omk

Go back to Chlorine Binding Sites List in 3omk
Chlorine binding site 1 out of 2 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:36.2
occ:1.00
CL25 A:OMK1 0.0 36.2 1.0
C22 A:OMK1 1.7 33.0 1.0
C23 A:OMK1 2.7 31.5 1.0
C24 A:OMK1 2.7 29.4 1.0
CZ A:PHE333 3.9 23.8 1.0
CE A:MET454 3.9 44.0 1.0
C19 A:OMK1 4.0 29.1 1.0
C18 A:OMK1 4.0 26.6 1.0
CD2 A:LEU455 4.0 34.0 1.0
CE1 A:HIS451 4.1 39.7 0.5
CD2 A:LEU291 4.1 32.1 1.0
SD A:MET454 4.2 47.8 1.0
CE1 A:PHE333 4.2 25.1 1.0
CG A:MET454 4.2 42.3 1.0
CZ3 A:TRP458 4.4 30.8 1.0
ND1 A:HIS451 4.4 40.8 0.5
C12 A:OMK1 4.5 26.1 1.0
CD1 A:LEU291 4.6 28.4 1.0
CG A:LEU455 4.9 32.5 1.0
CE2 A:PHE333 4.9 25.6 1.0
CE A:MET332 4.9 33.0 1.0
CB A:MET454 5.0 37.7 1.0
CG A:LEU291 5.0 26.9 1.0

Chlorine binding site 2 out of 2 in 3omk

Go back to Chlorine Binding Sites List in 3omk
Chlorine binding site 2 out of 2 in the Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Fxr in Complex with (2S)-2-[2-(4- Chlorophenyl)-5,6-Difluoro-1H-Benzimidazol-1-Yl]-2-Cyclohexyl-N-(2- Methylphenyl)Ethanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2

b:43.7
occ:1.00
CL25 C:OMK2 0.0 43.7 1.0
C22 C:OMK2 1.7 39.0 1.0
C24 C:OMK2 2.7 33.9 1.0
C23 C:OMK2 2.7 38.5 1.0
CZ C:PHE333 4.0 37.4 1.0
C18 C:OMK2 4.0 30.4 1.0
C19 C:OMK2 4.0 34.4 1.0
CD2 C:LEU291 4.2 36.8 1.0
CE1 C:PHE333 4.2 38.7 1.0
CD1 C:ILE361 4.3 38.2 1.0
CD2 C:LEU455 4.4 43.1 1.0
CZ3 C:TRP458 4.4 39.0 1.0
CG C:MET454 4.4 50.2 1.0
C12 C:OMK2 4.5 29.5 1.0
SD C:MET454 4.6 54.9 1.0
CD1 C:LEU291 4.7 33.5 1.0
CB C:MET454 4.9 45.7 1.0
SD C:MET369 5.0 51.7 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: Sat Dec 12 10:00:14 2020

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