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Fluorine in PDB 6b5h: ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)

Enzymatic activity of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)

All present enzymatic activity of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121):
1.2.1.36;

Protein crystallography data

The structure of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121), PDB code: 6b5h was solved by Y.Chen, J.-Y.Zhu, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.82 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.850, 141.860, 164.750, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) (pdb code 6b5h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121), PDB code: 6b5h:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6b5h

Go back to Fluorine Binding Sites List in 6b5h
Fluorine binding site 1 out of 4 in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:45.6
occ:1.00
 F24 A:CU4602 0.0 45.6 1.0
C23 A:CU4602 1.3 46.1 1.0
C22 A:CU4602 2.3 45.1 1.0
C25 A:CU4602 2.4 44.0 1.0
NE1 A:TRP195 3.3 31.6 1.0
OG1 A:THR146 3.3 25.8 1.0
CE A:MET495 3.4 37.9 1.0
C21 A:CU4602 3.6 47.2 1.0
C19 A:CU4602 3.7 44.5 1.0
O A:GLY142 3.8 20.4 1.0
N A:ALA479 3.9 41.8 1.0
CE2 A:TRP195 4.0 33.6 1.0
C A:ASN478 4.0 45.2 1.0
CZ2 A:TRP195 4.1 35.3 1.0
C20 A:CU4602 4.1 49.0 1.0
CA A:GLY142 4.1 20.5 1.0
CD1 A:LEU191 4.3 33.7 1.0
CA A:ALA479 4.3 38.9 1.0
C A:GLY142 4.4 21.1 1.0
CA A:ASN478 4.4 44.8 1.0
CD1 A:TRP195 4.4 31.8 1.0
O A:ASN478 4.4 44.0 1.0
N A:ASN478 4.7 47.0 1.0
CB A:THR146 4.7 24.2 1.0
CB A:ALA479 4.7 35.9 1.0
N18 A:CU4602 4.8 47.4 1.0
O17 A:CU4602 4.9 54.6 1.0
O A:HOH735 4.9 42.2 1.0
SD A:MET495 5.0 58.2 1.0

Fluorine binding site 2 out of 4 in 6b5h

Go back to Fluorine Binding Sites List in 6b5h
Fluorine binding site 2 out of 4 in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:58.3
occ:1.00
 F24 B:CU4602 0.0 58.3 1.0
C23 B:CU4602 1.3 62.5 1.0
C22 B:CU4602 2.3 60.9 1.0
C25 B:CU4602 2.4 60.0 1.0
NE1 B:TRP195 3.0 42.5 1.0
OG1 B:THR146 3.4 38.5 1.0
C21 B:CU4602 3.6 63.6 1.0
C19 B:CU4602 3.7 69.5 1.0
O B:GLY142 3.7 38.5 1.0
CE2 B:TRP195 3.7 47.8 1.0
CZ2 B:TRP195 3.7 52.8 1.0
CA B:GLY142 3.9 38.6 1.0
C20 B:CU4602 4.1 67.1 1.0
C B:GLY142 4.1 37.6 1.0
CD1 B:TRP195 4.2 43.1 1.0
N B:ALA479 4.2 56.4 1.0
CD1 B:LEU191 4.5 42.5 1.0
CA B:ALA479 4.5 55.2 1.0
C B:ASN478 4.5 57.8 1.0
CB B:ALA479 4.7 43.4 1.0
CB B:THR146 4.8 31.4 1.0
N18 B:CU4602 4.8 71.6 1.0
O B:ASN478 4.9 52.9 1.0
SD B:MET495 4.9 75.6 1.0
CA B:ASN478 5.0 56.8 1.0
O17 B:CU4602 5.0 68.3 1.0

Fluorine binding site 3 out of 4 in 6b5h

Go back to Fluorine Binding Sites List in 6b5h
Fluorine binding site 3 out of 4 in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:55.5
occ:1.00
 F24 C:CU4602 0.0 55.5 1.0
C23 C:CU4602 1.3 56.1 1.0
C22 C:CU4602 2.3 53.1 1.0
C25 C:CU4602 2.4 50.6 1.0
NE1 C:TRP195 3.1 40.3 1.0
OG1 C:THR146 3.3 37.6 1.0
C21 C:CU4602 3.6 52.7 1.0
CZ2 C:TRP195 3.6 49.9 1.0
C19 C:CU4602 3.7 57.6 1.0
CE2 C:TRP195 3.7 44.9 1.0
N C:ALA479 3.9 48.8 1.0
C C:ASN478 3.9 52.4 1.0
O C:GLY142 3.9 31.1 1.0
O C:ASN478 3.9 51.7 1.0
CA C:ALA479 4.1 48.0 1.0
C20 C:CU4602 4.1 54.0 1.0
CA C:GLY142 4.1 37.0 1.0
CD1 C:TRP195 4.3 41.1 1.0
C C:GLY142 4.4 34.8 1.0
CD1 C:LEU191 4.5 43.7 1.0
CA C:ASN478 4.6 54.3 1.0
CB C:ALA479 4.7 41.7 1.0
CB C:THR146 4.7 31.4 1.0
O17 C:CU4602 4.8 61.2 1.0
N18 C:CU4602 4.8 55.6 1.0
N C:ASN478 4.9 58.1 1.0
SD C:MET495 4.9 69.4 1.0
CH2 C:TRP195 5.0 51.2 1.0

Fluorine binding site 4 out of 4 in 6b5h

Go back to Fluorine Binding Sites List in 6b5h
Fluorine binding site 4 out of 4 in the ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of ALDH1A2 Liganded with Nad and 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3- [4-(Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:40.5
occ:1.00
 F24 D:CU4602 0.0 40.5 1.0
C23 D:CU4602 1.3 43.0 1.0
C22 D:CU4602 2.3 43.8 1.0
C25 D:CU4602 2.4 40.4 1.0
NE1 D:TRP195 3.1 27.8 1.0
OG1 D:THR146 3.2 26.7 1.0
C21 D:CU4602 3.6 45.2 1.0
C19 D:CU4602 3.7 46.6 1.0
O D:GLY142 3.8 21.4 1.0
CE2 D:TRP195 3.8 35.4 1.0
CZ2 D:TRP195 3.9 36.0 1.0
CE D:MET495 4.0 41.2 1.0
N D:ALA479 4.1 41.2 1.0
CA D:GLY142 4.1 23.9 1.0
C20 D:CU4602 4.1 48.1 1.0
C D:ASN478 4.2 41.0 1.0
CD1 D:TRP195 4.2 35.6 1.0
CD1 D:LEU191 4.3 28.7 1.0
C D:GLY142 4.3 22.0 1.0
CA D:ALA479 4.3 42.4 1.0
O D:ASN478 4.5 41.8 1.0
CB D:THR146 4.6 25.6 1.0
CB D:ALA479 4.7 34.5 1.0
CA D:ASN478 4.7 41.7 1.0
O17 D:CU4602 4.8 48.7 1.0
N18 D:CU4602 4.8 46.3 1.0

Reference:

Y.Chen, J.Y.Zhu, K.H.Hong, D.C.Mikles, G.I.Georg, A.S.Goldstein, J.K.Amory, E.Schonbrunn. Structural Basis of ALDH1A2 Inhibition By Irreversible and Reversible Small Molecule Inhibitors. Acs Chem. Biol. V. 13 582 2018.
ISSN: ESSN 1554-8937
PubMed: 29240402
DOI: 10.1021/ACSCHEMBIO.7B00685
Page generated: Tue Jul 15 09:57:43 2025

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