Fluorine in PDB 7jra: Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol

The structure of Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol, PDB code: 7jra was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.21 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.480, 81.710, 92.970, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.5

The structure of Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol (pdb code 7jra). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol, PDB code: 7jra:

Fluorine binding site 1 out of 1 in the Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Tnf-Alpha in Complex with 2-[5-(3-Chloro-4-{[(1R)-1-(2- Fluorophenyl)Ethyl]Amino}Quinolin-6-Yl)Pyrimidin-2-Yl]Propan-2-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:20.3 occ:1.00 F31 B:VGY301 0.0 20.3 1.0 C29 B:VGY301 1.4 17.8 1.0 C28 B:VGY301 2.3 16.1 1.0 C24 B:VGY301 2.3 14.9 1.0 H46 B:VGY301 2.5 12.1 0.0 H50 B:VGY301 2.6 16.1 0.0 C23 B:VGY301 2.8 12.1 1.0 H51 B:VGY301 2.8 12.1 0.0 H37 B:VGY301 3.3 12.4 0.0 C30 B:VGY301 3.3 12.0 1.0 CD1 A:ILE231 3.3 11.9 1.0 C25 B:VGY301 3.6 16.6 1.0 C27 B:VGY301 3.6 16.0 1.0 H52 B:VGY301 3.6 12.1 0.0 CD2 B:LEU133 3.6 15.8 1.0 CD1 B:LEU133 3.6 14.9 1.0 CG B:LEU133 4.0 15.3 1.0 C26 B:VGY301 4.1 18.2 1.0 H34 B:VGY301 4.1 12.2 0.0 CD2 A:LEU133 4.1 12.8 1.0 CB B:LEU133 4.1 10.1 1.0 N22 B:VGY301 4.2 9.4 1.0 H53 B:VGY301 4.2 12.1 0.0 C17 B:VGY301 4.3 12.4 1.0 H49 B:VGY301 4.5 16.0 0.0 H47 B:VGY301 4.5 16.6 0.0 C5 B:VGY301 4.5 12.1 1.0 N B:GLY198 4.6 11.2 1.0 O B:GLY198 4.7 14.4 1.0 C B:GLY198 4.7 15.9 1.0 CG1 A:ILE231 4.8 12.5 1.0 CA B:GLY198 4.8 11.0 1.0 C11 B:VGY301 4.9 9.6 1.0 H45 B:VGY301 4.9 9.3 0.0 N16 B:VGY301 4.9 14.6 1.0 C6 B:VGY301 5.0 11.9 1.0 CA B:LEU133 5.0 9.8 1.0

H.Y.Xiao, N.Li, J.J.Duan, B.Jiang, Z.Lu, K.Ngu, J.Tino, L.M.Kopcho, H.Lu, J.Chen, A.J.Tebben, S.Sheriff, C.Y.Chang, J.Yanchunas Jr., D.Calambur, M.Gao, D.J.Shuster, V.Susulic, J.H.Xie, V.R.Guarino, D.R.Wu, K.R.Gregor, C.B.Goldstine, J.Hynes Jr., J.E.Macor, L.Salter-Cid, J.R.Burke, P.J.Shaw, T.G.M.Dhar. Biologic-Like in Vivo Efficacy with Small Molecule Inhibitors of Tnf Alpha Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33261314
DOI: 10.1021/ACS.JMEDCHEM.0C01732