Fluorine in PDB 4o9s: Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand

The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand, PDB code: 4o9s was solved by Z.Wang, S.Johnstone, N.P.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	85.737, 85.737, 118.806, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 26.1

The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand (pdb code 4o9s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand, PDB code: 4o9s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:27.5 occ:1.00 F1 A:2RY201 0.0 27.5 1.0 C22 A:2RY201 1.3 27.4 1.0 F2 A:2RY201 2.1 27.4 1.0 F3 A:2RY201 2.2 27.5 1.0 C21 A:2RY201 2.3 27.2 1.0 C16 A:2RY201 2.9 27.1 1.0 C9 A:2RY201 3.0 26.9 1.0 N A:LEU37 3.0 29.6 1.0 C8 A:2RY201 3.3 26.7 1.0 CA A:PHE36 3.4 29.2 1.0 C20 A:2RY201 3.4 27.2 1.0 C A:PHE36 3.5 29.4 1.0 CG A:LEU37 3.5 29.9 1.0 O1 A:2RY201 3.5 26.6 1.0 CD1 A:PHE36 3.8 28.9 1.0 CD2 A:LEU37 3.9 29.9 1.0 CA A:LEU37 4.0 29.8 1.0 N4 A:2RY201 4.1 26.6 1.0 CB A:LEU37 4.2 29.9 1.0 CG A:PHE36 4.2 29.0 1.0 O A:HOH303 4.2 26.0 1.0 C17 A:2RY201 4.2 27.2 1.0 N A:PHE36 4.3 29.3 1.0 O A:LEU35 4.3 29.4 1.0 CB A:PHE36 4.4 29.1 1.0 CE1 A:PHE36 4.4 28.8 1.0 O A:PHE36 4.4 29.3 1.0 CD1 A:LEU37 4.6 29.9 1.0 C19 A:2RY201 4.6 27.2 1.0 C6 A:2RY201 4.7 26.6 1.0 C A:LEU35 4.7 29.3 1.0 C18 A:2RY201 4.9 27.2 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:27.4 occ:1.00 F2 A:2RY201 0.0 27.4 1.0 C22 A:2RY201 1.3 27.4 1.0 F3 A:2RY201 2.1 27.5 1.0 F1 A:2RY201 2.1 27.5 1.0 C21 A:2RY201 2.3 27.2 1.0 C20 A:2RY201 2.7 27.2 1.0 C A:PHE36 3.1 29.4 1.0 CA A:PHE36 3.2 29.2 1.0 N A:LEU37 3.3 29.6 1.0 N A:PHE36 3.4 29.3 1.0 O A:PHE36 3.5 29.3 1.0 C16 A:2RY201 3.6 27.1 1.0 CG1 A:VAL61 3.7 35.4 1.0 C A:LEU35 3.8 29.3 1.0 CG A:LEU35 3.8 29.5 1.0 O A:LEU35 3.9 29.4 1.0 C19 A:2RY201 4.1 27.2 1.0 CG2 A:VAL61 4.1 35.4 1.0 CA A:LEU37 4.2 29.8 1.0 CD2 A:LEU35 4.2 29.5 1.0 C9 A:2RY201 4.3 26.9 1.0 CD2 A:LEU37 4.5 29.9 1.0 CB A:LEU35 4.5 29.4 1.0 CB A:VAL61 4.6 35.4 1.0 CB A:PHE36 4.6 29.1 1.0 CG A:LEU37 4.6 29.9 1.0 CD1 A:LEU35 4.7 29.4 1.0 C17 A:2RY201 4.7 27.2 1.0 CA A:LEU35 4.8 29.4 1.0 C18 A:2RY201 4.9 27.2 1.0 O A:HOH303 5.0 26.0 1.0 CB A:LEU37 5.0 29.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:27.5 occ:1.00 F3 A:2RY201 0.0 27.5 1.0 C22 A:2RY201 1.3 27.4 1.0 F2 A:2RY201 2.1 27.4 1.0 F1 A:2RY201 2.2 27.5 1.0 C21 A:2RY201 2.3 27.2 1.0 C16 A:2RY201 3.0 27.1 1.0 C9 A:2RY201 3.1 26.9 1.0 C20 A:2RY201 3.4 27.2 1.0 CD2 A:LEU37 3.4 29.9 1.0 CE A:MET73 3.6 34.8 1.0 CG2 A:VAL61 3.9 35.4 1.0 CG A:LEU37 3.9 29.9 1.0 N A:LEU37 4.2 29.6 1.0 C8 A:2RY201 4.2 26.7 1.0 C17 A:2RY201 4.3 27.2 1.0 C19 A:2RY201 4.5 27.2 1.0 CG1 A:VAL61 4.6 35.4 1.0 C A:PHE36 4.6 29.4 1.0 CA A:LEU37 4.7 29.8 1.0 SD A:MET73 4.7 34.8 1.0 CB A:ALA71 4.8 37.0 1.0 O1 A:2RY201 4.8 26.6 1.0 CB A:LEU37 4.9 29.9 1.0 CB A:VAL61 4.9 35.4 1.0 CA A:PHE36 4.9 29.2 1.0 C18 A:2RY201 4.9 27.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:24.4 occ:1.00 F1 B:2RY201 0.0 24.4 1.0 C22 B:2RY201 1.3 24.4 1.0 F2 B:2RY201 2.1 24.4 1.0 F3 B:2RY201 2.2 24.4 1.0 C21 B:2RY201 2.3 24.4 1.0 C16 B:2RY201 2.9 24.4 1.0 C9 B:2RY201 3.0 24.3 1.0 N B:LEU37 3.1 28.2 1.0 C8 B:2RY201 3.4 24.3 1.0 CA B:PHE36 3.4 28.0 1.0 C20 B:2RY201 3.4 24.4 1.0 C B:PHE36 3.5 28.1 1.0 CG B:LEU37 3.5 28.4 1.0 O1 B:2RY201 3.5 24.2 1.0 CD1 B:PHE36 3.7 27.8 1.0 CD2 B:LEU37 4.0 28.4 1.0 CA B:LEU37 4.0 28.4 1.0 CG B:PHE36 4.1 27.8 1.0 N4 B:2RY201 4.2 24.4 1.0 CB B:LEU37 4.2 28.4 1.0 C17 B:2RY201 4.2 24.4 1.0 O B:HOH307 4.3 26.2 1.0 CE1 B:PHE36 4.3 27.8 1.0 CB B:PHE36 4.3 27.9 1.0 N B:PHE36 4.3 28.1 1.0 O B:PHE36 4.4 28.1 1.0 O B:LEU35 4.5 28.3 1.0 CD1 B:LEU37 4.5 28.4 1.0 C19 B:2RY201 4.6 24.4 1.0 C6 B:2RY201 4.7 24.4 1.0 C B:LEU35 4.7 28.3 1.0 C18 B:2RY201 4.9 24.4 1.0 CD2 B:PHE36 4.9 27.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:24.4 occ:1.00 F2 B:2RY201 0.0 24.4 1.0 C22 B:2RY201 1.3 24.4 1.0 F3 B:2RY201 2.1 24.4 1.0 F1 B:2RY201 2.1 24.4 1.0 C21 B:2RY201 2.3 24.4 1.0 C20 B:2RY201 2.7 24.4 1.0 C B:PHE36 3.1 28.1 1.0 CA B:PHE36 3.2 28.0 1.0 N B:LEU37 3.3 28.2 1.0 CG2 B:VAL61 3.4 34.5 1.0 N B:PHE36 3.5 28.1 1.0 O B:PHE36 3.5 28.1 1.0 C16 B:2RY201 3.6 24.4 1.0 CG B:LEU35 3.9 28.5 1.0 C B:LEU35 3.9 28.3 1.0 C19 B:2RY201 4.0 24.4 1.0 CB B:VAL61 4.1 34.5 1.0 O B:LEU35 4.1 28.3 1.0 CA B:LEU37 4.2 28.4 1.0 CD2 B:LEU35 4.3 28.5 1.0 C9 B:2RY201 4.3 24.3 1.0 CD2 B:LEU37 4.5 28.4 1.0 CG B:LEU37 4.6 28.4 1.0 CB B:PHE36 4.6 27.9 1.0 CB B:LEU35 4.7 28.5 1.0 C17 B:2RY201 4.7 24.4 1.0 CG1 B:VAL61 4.8 34.7 1.0 CD1 B:LEU35 4.8 28.6 1.0 C18 B:2RY201 4.9 24.4 1.0 CA B:LEU35 4.9 28.5 1.0 CB B:LEU37 4.9 28.4 1.0 O B:HOH307 5.0 26.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4)in Complex with A Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:24.4 occ:1.00 F3 B:2RY201 0.0 24.4 1.0 C22 B:2RY201 1.3 24.4 1.0 F2 B:2RY201 2.1 24.4 1.0 F1 B:2RY201 2.2 24.4 1.0 C21 B:2RY201 2.3 24.4 1.0 C16 B:2RY201 3.0 24.4 1.0 C9 B:2RY201 3.1 24.3 1.0 C20 B:2RY201 3.4 24.4 1.0 CD2 B:LEU37 3.5 28.4 1.0 CE B:MET73 3.6 32.7 1.0 CG B:LEU37 3.9 28.4 1.0 C8 B:2RY201 4.2 24.3 1.0 C17 B:2RY201 4.3 24.4 1.0 N B:LEU37 4.3 28.2 1.0 CG2 B:VAL61 4.5 34.5 1.0 CB B:ALA71 4.5 35.0 1.0 CB B:VAL61 4.5 34.5 1.0 C19 B:2RY201 4.6 24.4 1.0 C B:PHE36 4.6 28.1 1.0 SD B:MET73 4.7 32.7 1.0 CA B:LEU37 4.7 28.4 1.0 O1 B:2RY201 4.8 24.2 1.0 CG1 B:VAL61 4.8 34.7 1.0 CB B:LEU37 4.9 28.4 1.0 CA B:PHE36 4.9 28.0 1.0 C18 B:2RY201 4.9 24.4 1.0 CD1 B:LEU37 4.9 28.4 1.0

Y.Wang, R.Connors, P.Fan, X.Wang, Z.Wang, J.Liu, F.Kayser, J.C.Medina, S.Johnstone, H.Xu, S.Thibault, N.Walker, M.Conn, Y.Zhang, Q.Liu, M.P.Grillo, A.Motani, P.Coward, Z.Wang. Structure-Assisted Discovery of the First Non-Retinoid Ligands For Retinol-Binding Protein 4. Bioorg.Med.Chem.Lett. V. 24 2885 2014.
ISSN: ISSN 0960-894X
PubMed: 24835984
DOI: 10.1016/J.BMCL.2014.04.089