Fluorine in PDB 3abt: Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine

The structure of Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine, PDB code: 3abt was solved by S.Mimasu, N.Umezawa, S.Sato, T.Higuchi, T.Umehara, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.73 / 3.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.840, 183.840, 109.150, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 27.2

The binding sites of Fluorine atom in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine (pdb code 3abt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine, PDB code: 3abt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine


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 LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:62.4 occ:1.00 FAA A:2PF1 0.0 62.4 1.0 CAA A:2PF1 1.3 60.9 1.0 CAB A:2PF1 2.4 59.3 1.0 CAC A:2PF1 2.4 61.6 1.0 FAC A:2PF1 2.7 61.3 1.0 CBZ A:2PF1 2.8 56.3 1.0 O A:ALA809 2.9 41.5 1.0 CBK A:2PF1 3.2 52.3 1.0 NBJ A:2PF1 3.3 51.1 1.0 CZ A:TYR761 3.3 36.7 1.0 CE2 A:TYR761 3.4 36.7 1.0 NBL A:2PF1 3.4 51.7 1.0 CBR A:2PF1 3.5 53.9 1.0 CE1 A:TYR761 3.5 36.6 1.0 CBI A:2PF1 3.6 49.6 1.0 CAD A:2PF1 3.6 60.3 1.0 CAE A:2PF1 3.6 62.0 1.0 CD2 A:TYR761 3.7 36.2 1.0 OH A:TYR761 3.7 37.1 1.0 CD1 A:TYR761 3.9 36.3 1.0 CG A:TYR761 4.0 36.1 1.0 CBT A:2PF1 4.0 51.5 1.0 C A:ALA809 4.0 41.2 1.0 CAF A:2PF1 4.1 61.5 1.0 CCA A:2PF1 4.2 55.8 1.0 CBM A:2PF1 4.2 52.2 1.0 CB A:ALA809 4.4 41.0 1.0 CBU A:2PF1 4.5 52.3 1.0 CBP A:2PF1 4.5 53.3 1.0 NBS A:2PF1 4.5 54.0 1.0 NBO A:2PF1 4.7 52.7 1.0 FAE A:2PF1 4.7 63.0 1.0 FAB A:2PF1 4.8 60.9 1.0 CBV A:2PF1 4.8 51.6 1.0 CG2 A:THR810 4.8 40.2 1.0 CA A:ALA809 4.9 41.4 1.0 O A:ALA539 4.9 42.6 1.0 OBN A:2PF1 4.9 52.5 1.0 CA A:THR810 4.9 40.5 1.0 N A:THR810 4.9 40.9 1.0 CB A:TYR761 5.0 35.8 1.0 CCB A:2PF1 5.0 55.1 1.0

Fluorine binding site 2 out of 5 in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine


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 LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:60.9 occ:1.00 FAB A:2PF1 0.0 60.9 1.0 CAD A:2PF1 1.3 60.3 1.0 CAF A:2PF1 2.3 61.5 1.0 CAB A:2PF1 2.4 59.3 1.0 FAD A:2PF1 2.7 61.8 1.0 CCA A:2PF1 2.7 55.8 1.0 OBQ A:2PF1 2.8 53.3 1.0 CBZ A:2PF1 3.0 56.3 1.0 CBP A:2PF1 3.0 53.3 1.0 NBO A:2PF1 3.5 52.7 1.0 CB A:VAL333 3.5 40.9 1.0 CBR A:2PF1 3.6 53.9 1.0 CAE A:2PF1 3.6 62.0 1.0 CAA A:2PF1 3.6 60.9 1.0 CG2 A:VAL333 3.7 40.5 1.0 CCB A:2PF1 3.9 55.1 1.0 CAC A:2PF1 4.1 61.6 1.0 OCC A:2PF1 4.1 56.2 1.0 CG1 A:VAL333 4.3 40.6 1.0 CBM A:2PF1 4.4 52.2 1.0 NBS A:2PF1 4.4 54.0 1.0 CA A:VAL333 4.6 41.4 1.0 N A:VAL333 4.7 41.8 1.0 FAE A:2PF1 4.7 63.0 1.0 CBK A:2PF1 4.8 52.3 1.0 FAA A:2PF1 4.8 62.4 1.0 CZ A:PHE538 4.8 42.0 1.0 NBL A:2PF1 5.0 51.7 1.0

Fluorine binding site 3 out of 5 in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine


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 LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:61.3 occ:1.00 FAC A:2PF1 0.0 61.3 1.0 CAC A:2PF1 1.3 61.6 1.0 CAE A:2PF1 2.4 62.0 1.0 CAA A:2PF1 2.4 60.9 1.0 FAA A:2PF1 2.7 62.4 1.0 FAE A:2PF1 2.7 63.0 1.0 O A:ALA809 2.9 41.5 1.0 CG2 A:THR810 3.6 40.2 1.0 CAF A:2PF1 3.6 61.5 1.0 CAB A:2PF1 3.7 59.3 1.0 C A:ALA809 4.0 41.2 1.0 CAD A:2PF1 4.1 60.3 1.0 CB A:ALA809 4.2 41.0 1.0 O A:ALA539 4.4 42.6 1.0 CE2 A:TYR761 4.4 36.7 1.0 O A:PRO808 4.4 42.0 1.0 FAD A:2PF1 4.7 61.8 1.0 CA A:ALA809 4.8 41.4 1.0 CD2 A:TYR761 4.8 36.2 1.0 CBZ A:2PF1 4.9 56.3 1.0 CB A:THR810 4.9 40.3 1.0 CZ A:TYR761 4.9 36.7 1.0 N A:THR810 4.9 40.9 1.0 CA A:THR810 5.0 40.5 1.0

Fluorine binding site 4 out of 5 in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine


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 LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:61.8 occ:1.00 FAD A:2PF1 0.0 61.8 1.0 CAF A:2PF1 1.4 61.5 1.0 CAE A:2PF1 2.4 62.0 1.0 CAD A:2PF1 2.4 60.3 1.0 FAB A:2PF1 2.7 60.9 1.0 FAE A:2PF1 2.7 63.0 1.0 CG2 A:THR335 3.6 43.1 1.0 CAC A:2PF1 3.6 61.6 1.0 CAB A:2PF1 3.6 59.3 1.0 CAA A:2PF1 4.1 60.9 1.0 CG1 A:VAL333 4.4 40.6 1.0 CB A:VAL333 4.6 40.9 1.0 ND1 A:HIS564 4.7 52.2 1.0 CE1 A:HIS564 4.7 52.1 1.0 FAC A:2PF1 4.7 61.3 1.0 NBO A:2PF1 4.9 52.7 1.0 CBZ A:2PF1 5.0 56.3 1.0

Fluorine binding site 5 out of 5 in the Crystal Structure of LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine


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 LSD1 in Complex with Trans-2- Pentafluorophenylcyclopropylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:63.0 occ:1.00 FAE A:2PF1 0.0 63.0 1.0 CAE A:2PF1 1.3 62.0 1.0 CAC A:2PF1 2.4 61.6 1.0 CAF A:2PF1 2.4 61.5 1.0 FAD A:2PF1 2.7 61.8 1.0 FAC A:2PF1 2.7 61.3 1.0 CAA A:2PF1 3.6 60.9 1.0 CAD A:2PF1 3.6 60.3 1.0 CG2 A:THR335 4.0 43.1 1.0 CAB A:2PF1 4.2 59.3 1.0 CG2 A:THR810 4.6 40.2 1.0 FAB A:2PF1 4.7 60.9 1.0 FAA A:2PF1 4.7 62.4 1.0

S.Mimasu, N.Umezawa, S.Sato, T.Higuchi, T.Umehara, S.Yokoyama. Structurally Designed Trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1 Biochemistry V. 49 6494 2010.
ISSN: ISSN 0006-2960
PubMed: 20568732
DOI: 10.1021/BI100299R