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Fluorine in PDB 7jyr: Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine

Enzymatic activity of Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine

All present enzymatic activity of Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine:
2.7.10.1;

Protein crystallography data

The structure of Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine, PDB code: 7jyr was solved by A.P.Mcgrath, H.Zou, W.Lane, K.Saikatendu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.604, 56.89, 103.403, 90, 90, 90
R / Rfree (%) 21.4 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine (pdb code 7jyr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine, PDB code: 7jyr:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7jyr

Go back to Fluorine Binding Sites List in 7jyr
Fluorine binding site 1 out of 2 in the Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1601

b:47.9
occ:1.00
 F24 A:VTA1601 0.0 47.9 1.0
C23 A:VTA1601 1.4 45.3 1.0
C22 A:VTA1601 2.4 47.1 1.0
C25 A:VTA1601 2.4 48.9 1.0
HA3 A:GLY1269 2.7 47.5 1.0
HB2 A:ASP1270 2.7 52.0 1.0
HA A:ASN1254 2.8 43.8 1.0
C A:GLY1269 3.0 41.6 1.0
HG A:LEU1256 3.0 47.8 1.0
O A:ASN1254 3.1 35.8 1.0
HD11 A:LEU1256 3.2 49.5 1.0
CA A:GLY1269 3.2 39.0 1.0
C A:ASN1254 3.2 36.4 1.0
N A:ASP1270 3.2 43.2 1.0
O A:GLY1269 3.3 45.2 1.0
HB3 A:ASP1270 3.4 52.0 1.0
CB A:ASP1270 3.4 42.7 1.0
H A:GLY1269 3.4 47.2 1.0
CA A:ASN1254 3.5 35.9 1.0
H A:ASP1270 3.5 52.6 1.0
C21 A:VTA1601 3.6 50.5 1.0
C26 A:VTA1601 3.6 53.8 1.0
HD21 A:LEU1256 3.8 55.6 1.0
CG A:LEU1256 3.8 39.2 1.0
N A:GLY1269 3.8 38.7 1.0
CD1 A:LEU1256 3.8 40.6 1.0
CA A:ASP1270 3.9 44.2 1.0
N A:CYS1255 4.0 35.3 1.0
HB3 A:ASN1254 4.0 42.9 1.0
HD12 A:LEU1256 4.1 49.5 1.0
HA2 A:GLY1269 4.1 47.5 1.0
C20 A:VTA1601 4.1 55.7 1.0
O A:ARG1253 4.1 38.4 1.0
HA A:ASP1270 4.2 53.8 1.0
CD2 A:LEU1256 4.2 45.7 1.0
HA A:CYS1255 4.3 48.2 1.0
CB A:ASN1254 4.3 35.1 1.0
H A:CYS1255 4.5 43.2 1.0
CA A:CYS1255 4.5 39.5 1.0
C A:CYS1255 4.5 41.3 1.0
HD23 A:LEU1256 4.5 55.6 1.0
N A:ASN1254 4.6 37.5 1.0
O A:CYS1255 4.7 37.8 1.0
HD13 A:LEU1256 4.7 49.5 1.0
F27 A:VTA1601 4.7 55.5 1.0
OD1 A:ASN1254 4.7 44.5 1.0
CG A:ASP1270 4.7 47.5 1.0
C A:ARG1253 4.8 40.6 1.0
N A:LEU1256 4.9 41.7 1.0

Fluorine binding site 2 out of 2 in 7jyr

Go back to Fluorine Binding Sites List in 7jyr
Fluorine binding site 2 out of 2 in the Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Halk in Complex with 1-[(1R,2R)-1-(2,4-Difluorophenyl)-2-[2-(5-Methyl- 1H-Pyrazol-3-Yl)-4-(Trifluoromethyl)Phenoxy]Cyclopropyl]Methanamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1601

b:55.5
occ:1.00
 F27 A:VTA1601 0.0 55.5 1.0
C26 A:VTA1601 1.4 53.8 1.0
C25 A:VTA1601 2.3 48.9 1.0
C20 A:VTA1601 2.4 55.7 1.0
HG21 A:VAL1130 2.7 76.3 1.0
C17 A:VTA1601 2.7 81.4 1.0
C18 A:VTA1601 2.9 59.0 1.0
O14 A:VTA1601 3.1 53.0 1.0
C15 A:VTA1601 3.3 69.2 1.0
C3 A:VTA1601 3.5 45.6 1.0
HG11 A:VAL1130 3.5 69.0 1.0
C23 A:VTA1601 3.6 45.3 1.0
CG2 A:VAL1130 3.6 63.0 1.0
C21 A:VTA1601 3.6 50.5 1.0
HD21 A:LEU1256 3.9 55.6 1.0
HG22 A:VAL1130 4.0 76.3 1.0
HG23 A:VAL1130 4.1 76.3 1.0
C22 A:VTA1601 4.1 47.1 1.0
HD11 A:LEU1256 4.2 49.5 1.0
C1 A:VTA1601 4.2 47.1 1.0
C2 A:VTA1601 4.2 42.7 1.0
CG1 A:VAL1130 4.3 56.8 1.0
HB A:VAL1130 4.4 76.0 1.0
CB A:VAL1130 4.4 62.7 1.0
C13 A:VTA1601 4.4 49.6 1.0
HD2 A:LYS1150 4.5 103.1 1.0
C4 A:VTA1601 4.6 46.3 1.0
HG13 A:VAL1130 4.7 69.0 1.0
F24 A:VTA1601 4.7 47.9 1.0
HZ3 A:LYS1150 4.8 109.3 1.0
CD2 A:LEU1256 4.8 45.7 1.0
CD1 A:LEU1256 5.0 40.6 1.0

Reference:

I.Fujimori, T.Wakabayashi, M.Murakami, A.Okabe, T.Ishii, A.Mcgrath, H.Zou, K.S.Saikatendu, H.Imoto. Discovery of Novel and Highly Selective Cyclopropane Alk Inhibitors Through A Fragment-Assisted, Structure-Based Drug Design. Acs Omega V. 5 31984 2020.
ISSN: ESSN 2470-1343
PubMed: 33344853
DOI: 10.1021/ACSOMEGA.0C04900
Page generated: Tue Jul 15 20:40:37 2025

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