Fluorine in PDB 6fmf: Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure

The structure of Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure, PDB code: 6fmf was solved by T.Yelland, S.Djordjevic, D.Selwood, I.Zachary, P.Frankel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.67 / 2.81
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	39.655, 39.655, 91.780, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 29.2

The binding sites of Fluorine atom in the Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure (pdb code 6fmf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure, PDB code: 6fmf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:51.0 occ:1.00 F1 A:TFA502 0.0 51.0 1.0 C2 A:TFA502 1.3 54.4 1.0 F2 A:TFA502 2.2 49.0 1.0 F3 A:TFA502 2.2 60.0 1.0 C1 A:TFA502 2.3 50.5 1.0 OXT A:TFA502 2.7 51.8 1.0 O A:TFA502 3.4 49.9 1.0 NE2 A:GLN296 3.5 35.4 1.0 CA A:SER298 3.6 35.9 1.0 N A:THR299 4.0 35.2 1.0 C A:SER298 4.1 36.2 1.0 CG A:GLN296 4.4 35.6 1.0 CD A:GLN296 4.4 33.8 1.0 N A:SER298 4.5 37.3 1.0 CB A:SER298 4.5 37.5 1.0 O A:TYR297 4.5 42.0 1.0 CG2 A:THR299 4.6 35.2 1.0 C A:TYR297 4.8 38.8 1.0 O A:SER298 4.9 37.2 1.0

Fluorine binding site 2 out of 3 in the Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:49.0 occ:1.00 F2 A:TFA502 0.0 49.0 1.0 C2 A:TFA502 1.3 54.4 1.0 F3 A:TFA502 2.1 60.0 1.0 F1 A:TFA502 2.2 51.0 1.0 C1 A:TFA502 2.3 50.5 1.0 O A:TFA502 2.6 49.9 1.0 O A:TYR297 3.0 42.0 1.0 CA A:SER298 3.2 35.9 1.0 OXT A:TFA502 3.4 51.8 1.0 CB A:SER298 3.5 37.5 1.0 C A:TYR297 3.8 38.8 1.0 N A:SER298 3.9 37.3 1.0 C A:SER298 4.3 36.2 1.0 N A:THR299 4.5 35.2 1.0 O A:GLN296 4.8 32.4 1.0 OG A:SER298 4.9 38.4 1.0

Fluorine binding site 3 out of 3 in the Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Neuropilin-1 B1 Domain in Complex with EG01377; 2.8 Angstrom Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:60.0 occ:1.00 F3 A:TFA502 0.0 60.0 1.0 C2 A:TFA502 1.3 54.4 1.0 F2 A:TFA502 2.1 49.0 1.0 F1 A:TFA502 2.2 51.0 1.0 C1 A:TFA502 2.3 50.5 1.0 OXT A:TFA502 2.9 51.8 1.0 O A:TFA502 3.0 49.9 1.0 CA A:SER298 5.0 35.9 1.0

J.Powell, F.Mota, D.Steadman, C.Soudy, J.T.Miyauchi, S.Crosby, A.Jarvis, T.Reisinger, N.Winfield, G.Evans, A.Finniear, T.Yelland, Y.T.Chou, A.W.E.Chan, A.O'leary, L.Cheng, D.Liu, C.Fotinou, C.Milagre, J.F.Martin, H.Jia, P.Frankel, S.Djordjevic, S.E.Tsirka, I.C.Zachary, D.L.Selwood. Small Molecule Neuropilin-1 Antagonists Combine Antiangiogenic and Antitumor Activity with Immune Modulation Through Reduction of Transforming Growth Factor Beta (Tgf Beta ) Production in Regulatory T-Cells. J. Med. Chem. V. 61 4135 2018.
ISSN: ISSN 1520-4804
PubMed: 29648813
DOI: 10.1021/ACS.JMEDCHEM.8B00210