Fluorine in PDB 6b5i: ALDH1A2 Liganded with 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3-[4- (Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121)

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

All present enzymatic activity of ALDH1A2 Liganded with 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 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3-[4- (Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121), PDB code: 6b5i 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) 81.54 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.830, 139.470, 163.070, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the ALDH1A2 Liganded with 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3-[4- (Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121) (pdb code 6b5i). 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 1-(4-Cyanophenyl)-N-(3-Fluorophenyl)-3-[4- (Methylsulfonyl)Phenyl]-1H-Pyrazole-4-Carboxamide (Compound CM121), PDB code: 6b5i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6b5i

Go back to Fluorine Binding Sites List in 6b5i
Fluorine binding site 1 out of 4 in the ALDH1A2 Liganded with 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 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:F601

b:38.8
occ:1.00
 F24 A:CU4601 0.0 38.8 1.0
C23 A:CU4601 1.3 44.0 1.0
C25 A:CU4601 2.3 42.7 1.0
C22 A:CU4601 2.4 41.9 1.0
NE1 A:TRP195 3.2 37.0 1.0
OG1 A:THR146 3.3 23.2 1.0
C21 A:CU4601 3.6 43.5 1.0
C19 A:CU4601 3.6 49.4 1.0
CZ2 A:TRP195 3.7 37.5 1.0
CE2 A:TRP195 3.8 34.7 1.0
O A:GLY142 3.8 25.1 1.0
N A:ALA479 3.9 34.6 1.0
CA A:GLY142 4.0 26.2 1.0
C A:ASN478 4.0 43.6 1.0
CE A:MET495 4.1 41.0 1.0
C20 A:CU4601 4.1 43.4 1.0
CA A:ALA479 4.2 32.1 1.0
C A:GLY142 4.3 26.3 1.0
O A:ASN478 4.3 48.4 1.0
CD1 A:TRP195 4.4 31.0 1.0
CB A:ALA479 4.4 29.4 1.0
CA A:ASN478 4.6 46.1 1.0
CB A:THR146 4.7 26.8 1.0
CD1 A:LEU191 4.7 26.1 1.0
O17 A:CU4601 4.8 42.3 1.0
N18 A:CU4601 4.8 52.2 1.0
N A:ASN478 4.9 45.5 1.0
CH2 A:TRP195 5.0 38.9 1.0

Fluorine binding site 2 out of 4 in 6b5i

Go back to Fluorine Binding Sites List in 6b5i
Fluorine binding site 2 out of 4 in the ALDH1A2 Liganded with 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 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:F601

b:48.7
occ:1.00
 F24 B:CU4601 0.0 48.7 1.0
C23 B:CU4601 1.3 54.9 1.0
C22 B:CU4601 2.3 52.7 1.0
C25 B:CU4601 2.4 61.3 1.0
NE1 B:TRP195 3.3 46.8 1.0
OG1 B:THR146 3.4 35.0 1.0
C21 B:CU4601 3.6 58.7 1.0
C19 B:CU4601 3.7 64.6 1.0
CZ2 B:TRP195 3.7 55.8 1.0
N B:ALA479 3.8 49.9 1.0
O B:GLY142 3.8 36.5 1.0
CE2 B:TRP195 3.8 52.1 1.0
SD B:MET495 3.9 83.3 1.0
C B:ASN478 4.0 55.2 1.0
CA B:ALA479 4.0 51.3 1.0
CA B:GLY142 4.0 44.9 1.0
C20 B:CU4601 4.1 57.9 1.0
O B:ASN478 4.3 52.8 1.0
CB B:ALA479 4.3 41.9 1.0
C B:GLY142 4.4 39.9 1.0
CD1 B:TRP195 4.5 45.4 1.0
CA B:ASN478 4.5 53.9 1.0
CG B:MET495 4.7 63.4 1.0
CB B:THR146 4.8 33.5 1.0
N18 B:CU4601 4.9 64.3 1.0
CD1 B:LEU191 4.9 40.9 1.0
N B:ASN478 4.9 58.5 1.0
CH2 B:TRP195 5.0 60.5 1.0

Fluorine binding site 3 out of 4 in 6b5i

Go back to Fluorine Binding Sites List in 6b5i
Fluorine binding site 3 out of 4 in the ALDH1A2 Liganded with 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 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:F601

b:52.8
occ:1.00
 F24 C:CU4601 0.0 52.8 1.0
C23 C:CU4601 1.3 53.5 1.0
C22 C:CU4601 2.3 51.1 1.0
C25 C:CU4601 2.4 57.5 1.0
OG1 C:THR146 3.0 33.4 1.0
NE1 C:TRP195 3.0 45.8 1.0
O C:GLY142 3.6 42.3 1.0
CZ2 C:TRP195 3.6 63.4 1.0
CE2 C:TRP195 3.6 48.3 1.0
C21 C:CU4601 3.6 61.8 1.0
C19 C:CU4601 3.7 61.7 1.0
CA C:GLY142 3.9 49.7 1.0
N C:ALA479 4.0 55.5 1.0
C C:GLY142 4.1 40.5 1.0
C20 C:CU4601 4.1 61.5 1.0
SD C:MET495 4.2 63.1 1.0
CD1 C:TRP195 4.2 40.4 1.0
C C:ASN478 4.2 56.0 1.0
CD1 C:LEU191 4.3 38.4 1.0
CB C:THR146 4.4 36.6 1.0
CA C:ALA479 4.4 51.9 1.0
O C:ASN478 4.5 48.7 1.0
CA C:ASN478 4.7 58.2 1.0
CB C:ALA479 4.8 41.2 1.0
CH2 C:TRP195 4.8 64.3 1.0
CD2 C:TRP195 4.8 53.6 1.0
N18 C:CU4601 4.9 61.4 1.0
CE C:MET495 4.9 53.2 1.0
N C:THR146 4.9 35.0 1.0
CG C:LEU191 5.0 41.7 1.0

Fluorine binding site 4 out of 4 in 6b5i

Go back to Fluorine Binding Sites List in 6b5i
Fluorine binding site 4 out of 4 in the ALDH1A2 Liganded with 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 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:F601

b:44.3
occ:1.00
 F24 D:CU4601 0.0 44.3 1.0
C23 D:CU4601 1.3 44.6 1.0
C25 D:CU4601 2.3 41.9 1.0
C22 D:CU4601 2.4 44.1 1.0
OG1 D:THR146 3.4 20.9 1.0
NE1 D:TRP195 3.5 34.9 1.0
C21 D:CU4601 3.6 48.5 1.0
C19 D:CU4601 3.6 46.6 1.0
N D:ALA479 3.7 47.1 1.0
C D:ASN478 3.7 50.5 1.0
O D:GLY142 3.9 25.8 1.0
O D:ASN478 3.9 52.2 1.0
CA D:GLY142 4.0 27.7 1.0
CE D:MET495 4.1 43.4 1.0
CA D:ALA479 4.1 44.2 1.0
C20 D:CU4601 4.1 46.6 1.0
CE2 D:TRP195 4.2 36.9 1.0
CZ2 D:TRP195 4.3 35.8 1.0
C D:GLY142 4.3 23.5 1.0
CB D:ALA479 4.4 37.7 1.0
CA D:ASN478 4.4 51.4 1.0
CD1 D:TRP195 4.6 33.3 1.0
N D:ASN478 4.7 57.9 1.0
CD1 D:LEU191 4.7 28.2 1.0
CB D:THR146 4.8 23.2 1.0
O17 D:CU4601 4.8 45.0 1.0
N18 D:CU4601 4.8 49.0 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: Sun Dec 13 12:45:05 2020

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