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Fluorine in PDB 6dum: ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)

Enzymatic activity of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)

All present enzymatic activity of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G):
1.2.1.36;

Protein crystallography data

The structure of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G), PDB code: 6dum was solved by C.D.Buchman, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.802, 108.802, 82.877, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.9

Other elements in 6dum:

The structure of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) also contains other interesting chemical elements:

Ytterbium (Yb) 2 atoms
Chlorine (Cl) 7 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) (pdb code 6dum). 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 ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G), PDB code: 6dum:

Fluorine binding site 1 out of 1 in 6dum

Go back to Fluorine Binding Sites List in 6dum
Fluorine binding site 1 out of 1 in the ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of ALDH1A1 N121S in Complex with 6-{[(3-Fluorophenyl)Methyl]Sulfanyl}-2- (Oxetan-3-Yl)-5-Phenyl-2,5-Dihydro-4H-Pyrazolo[3,4-D]Pyrimidin-4-One (Compound 13G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:88.2
occ:1.00
 F24 A:A5Y603 0.0 88.2 1.0
C20 A:A5Y603 1.3 89.1 1.0
C19 A:A5Y603 2.3 92.9 1.0
C21 A:A5Y603 2.4 93.2 1.0
OG1 A:THR129 2.4 46.4 1.0
O A:GLY125 3.1 43.6 1.0
NE1 A:TRP178 3.2 49.2 1.0
C A:GLY125 3.5 45.6 1.0
C18 A:A5Y603 3.6 91.2 1.0
CA A:GLY125 3.6 45.0 1.0
C22 A:A5Y603 3.6 95.2 1.0
CB A:THR129 3.8 42.6 1.0
CD1 A:TRP178 4.1 47.1 1.0
C23 A:A5Y603 4.1 93.7 1.0
CE2 A:TRP178 4.1 49.8 1.0
CZ2 A:TRP178 4.4 54.4 1.0
N A:CYS126 4.4 47.4 1.0
CG2 A:THR129 4.5 41.6 1.0
CG1 A:VAL174 4.6 44.4 1.0
CA A:THR129 4.8 42.0 1.0
N A:THR129 4.8 42.4 1.0
O A:HOH829 4.8 40.7 1.0
C17 A:A5Y603 4.8 88.9 1.0

Reference:

B.C.Huddle, E.Grimley, C.D.Buchman, M.Chtcherbinine, B.Debnath, P.Mehta, K.Yang, C.A.Morgan, S.Li, J.Felton, D.Sun, G.Mehta, N.Neamati, R.J.Buckanovich, T.D.Hurley, S.D.Larsen. Structure-Based Optimization of A Novel Class of Aldehyde Dehydrogenase 1A (ALDH1A) Subfamily-Selective Inhibitors As Potential Adjuncts to Ovarian Cancer Chemotherapy. J.Med.Chem. V. 61 8754 2018.
ISSN: ISSN 0022-2623
PubMed: 30221940
DOI: 10.1021/ACS.JMEDCHEM.8B00930
Page generated: Tue Jul 15 10:52:37 2025

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