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

Protein crystallography data

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

Fluorine Binding Sites:

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 6fmf

Go back to Fluorine Binding Sites List in 6fmf
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 6fmf

Go back to Fluorine Binding Sites List in 6fmf
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 6fmf

Go back to Fluorine Binding Sites List in 6fmf
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

Reference:

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
Page generated: Sun Dec 13 12:50:18 2020

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