Fluorine in PDB 4ty9: An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline

The structure of An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline, PDB code: 4ty9 was solved by W.Shui, C.Yang, J.Lin, X.Chen, S.Qin, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.79 / 2.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.774, 101.643, 251.582, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.3

The binding sites of Fluorine atom in the An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline (pdb code 4ty9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline, PDB code: 4ty9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:80.2 occ:1.00 F01 A:3B0601 0.0 80.2 1.0 C04 A:3B0601 1.3 83.6 1.0 F A:3B0601 2.1 88.5 1.0 F02 A:3B0601 2.2 77.8 1.0 C02 A:3B0601 2.3 82.7 1.0 OE1 A:GLU481 2.6 32.2 1.0 C03 A:3B0601 2.8 82.0 1.0 CB A:GLU481 3.2 33.4 1.0 CA A:GLU481 3.3 33.7 1.0 CD A:GLU481 3.4 33.9 1.0 C05 A:3B0601 3.5 80.1 1.0 N A:GLU481 3.5 31.6 1.0 NH2 A:ARG484 3.6 33.5 1.0 CG A:GLU481 3.8 34.4 1.0 CZ A:ARG484 4.1 34.0 1.0 ND2 A:ASN369 4.1 27.6 1.0 C01 A:3B0601 4.2 82.0 1.0 CB A:SER371 4.2 29.8 1.0 C A:GLY480 4.2 32.8 1.0 OG A:SER478 4.3 35.4 1.0 CG2 A:THR385 4.3 23.5 1.0 OG A:SER371 4.4 30.6 1.0 OE2 A:GLU481 4.4 37.6 1.0 NE A:ARG484 4.4 35.8 1.0 O A:GLY480 4.6 31.2 1.0 N01 A:3B0601 4.6 79.2 1.0 NH1 A:ARG484 4.7 33.3 1.0 C A:GLU481 4.7 35.5 1.0 C A:3B0601 4.9 81.8 1.0 OD1 A:ASN369 4.9 24.6 1.0 CG A:ASN369 5.0 25.7 1.0

Fluorine binding site 2 out of 3 in the An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:77.8 occ:1.00 F02 A:3B0601 0.0 77.8 1.0 C04 A:3B0601 1.3 83.6 1.0 F01 A:3B0601 2.2 80.2 1.0 F A:3B0601 2.2 88.5 1.0 C02 A:3B0601 2.3 82.7 1.0 C05 A:3B0601 2.6 80.1 1.0 CB A:SER371 3.1 29.8 1.0 OE1 A:GLU361 3.2 44.2 1.0 OG A:SER371 3.2 30.6 1.0 OG A:SER478 3.4 35.4 1.0 C03 A:3B0601 3.6 82.0 1.0 CA A:SER371 3.9 29.0 1.0 N01 A:3B0601 4.0 79.2 1.0 CB A:GLU481 4.1 33.4 1.0 ND2 A:ASN369 4.2 27.6 1.0 CB A:SER478 4.2 33.8 1.0 CD A:GLU361 4.2 39.9 1.0 N A:GLU481 4.3 31.6 1.0 O A:VAL370 4.4 24.7 1.0 CA A:GLU481 4.6 33.7 1.0 OE1 A:GLU481 4.6 32.2 1.0 C01 A:3B0601 4.7 82.0 1.0 C A:3B0601 4.8 81.8 1.0 CB A:GLU361 4.8 30.2 1.0 N A:SER371 4.8 29.1 1.0 CG A:GLU361 4.9 33.8 1.0 C A:VAL370 5.0 26.9 1.0

Fluorine binding site 3 out of 3 in the An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of An Ligand-Observed Mass Spectrometry-Based Approach Integrated Into the Fragment Based Lead Discovery Pipeline within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:88.5 occ:1.00 F A:3B0601 0.0 88.5 1.0 C04 A:3B0601 1.3 83.6 1.0 F01 A:3B0601 2.1 80.2 1.0 F02 A:3B0601 2.2 77.8 1.0 ND2 A:ASN369 2.3 27.6 1.0 C02 A:3B0601 2.3 82.7 1.0 C03 A:3B0601 2.9 82.0 1.0 C05 A:3B0601 3.3 80.1 1.0 CG A:ASN369 3.3 25.7 1.0 OD1 A:ASN369 3.7 24.6 1.0 O A:GLU361 3.9 27.6 1.0 NH2 A:ARG484 3.9 33.5 1.0 O A:VAL370 3.9 24.7 1.0 CB A:SER371 4.0 29.8 1.0 C01 A:3B0601 4.2 82.0 1.0 OE1 A:GLU481 4.2 32.2 1.0 CG2 A:THR385 4.3 23.5 1.0 CZ A:ARG484 4.4 34.0 1.0 N01 A:3B0601 4.5 79.2 1.0 NH1 A:ARG484 4.5 33.3 1.0 CB A:ASN369 4.6 25.3 1.0 OE1 A:GLU361 4.6 44.2 1.0 C A:VAL370 4.6 26.9 1.0 CA A:SER371 4.7 29.0 1.0 OG A:SER371 4.7 30.6 1.0 C A:3B0601 4.8 81.8 1.0 C A:GLU361 4.9 25.3 1.0 CB A:GLU361 4.9 30.2 1.0 N A:SER371 4.9 29.1 1.0 O A:ASN369 5.0 29.6 1.0

X.Chen, S.Qin, S.Chen, J.Li, L.Li, Z.Wang, Q.Wang, J.Lin, C.Yang, W.Shui. A Ligand-Observed Mass Spectrometry Approach Integrated Into the Fragment Based Lead Discovery Pipeline Sci Rep V. 5 8361 2015.
ISSN: ESSN 2045-2322
PubMed: 25666181
DOI: 10.1038/SREP08361