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Fluorine in PDB 4qmv: MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide

Enzymatic activity of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide

All present enzymatic activity of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide:
2.7.11.1;

Protein crystallography data

The structure of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide, PDB code: 4qmv was solved by S.H.Olesen, C.Watts, J.-Y.Zhu, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.080, 57.850, 61.780, 90.00, 93.98, 90.00
R / Rfree (%) 16.7 / 22.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide (pdb code 4qmv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide, PDB code: 4qmv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4qmv

Go back to Fluorine Binding Sites List in 4qmv
Fluorine binding site 1 out of 3 in the MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.3
occ:1.00
 F32 A:34W401 0.0 27.3 1.0
C31 A:34W401 1.4 25.0 1.0
F34 A:34W401 2.2 22.3 1.0
F33 A:34W401 2.2 23.5 1.0
C23 A:34W401 2.4 23.2 1.0
O A:HOH589 3.0 32.4 1.0
C24 A:34W401 3.1 25.9 1.0
N26 A:34W401 3.1 29.4 1.0
C22 A:34W401 3.4 24.1 1.0
CD1 A:LEU151 3.5 23.6 1.0
CB A:ALA161 3.7 25.9 1.0
CG2 A:THR83 4.3 22.5 1.0
N25 A:34W401 4.3 25.5 1.0
C27 A:34W401 4.5 30.4 1.0
N21 A:34W401 4.6 22.9 1.0
O A:HOH579 4.7 30.1 1.0
CG A:LEU151 4.9 23.3 1.0
N A:ASP162 4.9 28.1 1.0
CA A:ALA161 4.9 29.5 1.0
CB A:THR83 4.9 27.4 1.0
CE A:MET99 4.9 32.9 1.0
C28 A:34W401 4.9 33.4 1.0
OG1 A:THR83 5.0 30.8 1.0
C20 A:34W401 5.0 26.5 1.0

Fluorine binding site 2 out of 3 in 4qmv

Go back to Fluorine Binding Sites List in 4qmv
Fluorine binding site 2 out of 3 in the MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:23.5
occ:1.00
 F33 A:34W401 0.0 23.5 1.0
C31 A:34W401 1.4 25.0 1.0
F34 A:34W401 2.2 22.3 1.0
F32 A:34W401 2.2 27.3 1.0
C23 A:34W401 2.3 23.2 1.0
C24 A:34W401 3.0 25.9 1.0
N26 A:34W401 3.0 29.4 1.0
C22 A:34W401 3.4 24.1 1.0
CG1 A:VAL38 3.8 26.9 1.0
CB A:ALA51 3.9 21.2 1.0
CG A:MET99 4.0 22.7 1.0
CB A:MET99 4.1 28.8 1.0
O A:HOH589 4.3 32.4 1.0
C27 A:34W401 4.3 30.4 1.0
N25 A:34W401 4.3 25.5 1.0
N21 A:34W401 4.6 22.9 1.0
CG2 A:VAL38 4.6 31.5 1.0
C28 A:34W401 4.7 33.4 1.0
CB A:VAL38 4.8 31.4 1.0
C20 A:34W401 4.9 26.5 1.0
CE A:MET99 5.0 32.9 1.0

Fluorine binding site 3 out of 3 in 4qmv

Go back to Fluorine Binding Sites List in 4qmv
Fluorine binding site 3 out of 3 in the MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of MST3 in Complex with Pf-03814735, N-{2-[(1S,4R)-6-{[4- (Cyclobutylamino)-5-(Trifluoromethyl)Pyrimidin-2-Yl]Amino}-1,2,3,4- Tetrahydro-1,4-Epiminonaphthalen-9-Yl]-2-Oxoethyl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:22.3
occ:1.00
 F34 A:34W401 0.0 22.3 1.0
C31 A:34W401 1.4 25.0 1.0
F32 A:34W401 2.2 27.3 1.0
F33 A:34W401 2.2 23.5 1.0
C23 A:34W401 2.4 23.2 1.0
C22 A:34W401 2.7 24.1 1.0
O A:GLU100 3.3 23.9 1.0
CB A:MET99 3.4 28.8 1.0
C24 A:34W401 3.7 25.9 1.0
CG A:MET99 3.9 22.7 1.0
N21 A:34W401 4.0 22.9 1.0
CE A:MET99 4.0 32.9 1.0
CB A:ALA51 4.0 21.2 1.0
O A:HOH589 4.1 32.4 1.0
CG2 A:THR83 4.2 22.5 1.0
CB A:THR83 4.3 27.4 1.0
N26 A:34W401 4.3 29.4 1.0
CD1 A:LEU151 4.5 23.6 1.0
C A:GLU100 4.5 23.7 1.0
CA A:MET99 4.7 26.6 1.0
OG1 A:THR83 4.7 30.8 1.0
N A:GLU100 4.7 27.0 1.0
N25 A:34W401 4.7 25.5 1.0
C A:MET99 4.8 24.4 1.0
SD A:MET99 4.8 32.4 1.0
C20 A:34W401 4.9 26.5 1.0

Reference:

S.H.Olesen, J.Y.Zhu, M.P.Martin, E.Schonbrunn. Discovery of Diverse Small-Molecule Inhibitors of Mammalian STERILE20-Like Kinase 3 (MST3). Chemmedchem V. 11 1137 2016.
ISSN: ISSN 1860-7179
PubMed: 27135311
DOI: 10.1002/CMDC.201600115
Page generated: Tue Jul 15 00:30:34 2025

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