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Fluorine in PDB 6fex: DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%

Enzymatic activity of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%

All present enzymatic activity of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%, PDB code: 6fex was solved by M.Stihle, H.Richter, J.Benz, B.Kuhn, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.47 / 1.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.834, 61.750, 63.072, 90.00, 106.51, 90.00
R / Rfree (%) 13.7 / 17.4

Other elements in 6fex:

The structure of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4% also contains other interesting chemical elements:

Bromine (Br) 1 atom
Iodine (I) 4 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4% (pdb code 6fex). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%, PDB code: 6fex:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6fex

Go back to Fluorine Binding Sites List in 6fex
Fluorine binding site 1 out of 3 in the DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:14.4
occ:1.00
 F14 A:D6Z1001 0.0 14.4 1.0
C13 A:D6Z1001 1.3 14.5 1.0
F15 A:D6Z1001 2.1 16.4 1.0
F16 A:D6Z1001 2.1 16.7 1.0
C12 A:D6Z1001 2.3 14.9 1.0
H43 A:D6Z1001 2.6 17.9 1.0
HE2 A:HIS764 2.8 11.9 1.0
N11 A:D6Z1001 2.9 14.2 1.0
HA A:ALA783 2.9 10.1 1.0
O A:ALA783 2.9 10.1 1.0
HB2 A:ASP784 3.0 13.7 1.0
C A:ALA783 3.0 9.4 1.0
HG22 A:ILE782 3.2 15.6 1.0
HD2 A:HIS764 3.2 11.2 1.0
H44 A:D6Z1001 3.2 17.9 1.0
NE2 A:HIS764 3.3 9.9 1.0
H42 A:D6Z1001 3.3 17.1 1.0
CA A:ALA783 3.4 8.4 1.0
CD2 A:HIS764 3.5 9.3 1.0
N A:ASP784 3.6 9.4 1.0
C9 A:D6Z1001 3.6 12.8 1.0
CB A:ASP784 3.7 11.4 1.0
HB3 A:ASP784 3.7 13.7 1.0
O10 A:D6Z1001 3.7 13.1 1.0
O A:ILE782 3.8 10.7 1.0
N A:ALA783 3.8 8.8 1.0
C A:ILE782 4.0 10.3 1.0
H A:ASP784 4.0 11.3 1.0
CG2 A:ILE782 4.1 13.0 1.0
CA A:ASP784 4.2 10.8 1.0
HG23 A:ILE684 4.3 15.6 1.0
H A:ALA783 4.3 10.5 1.0
HG21 A:ILE782 4.4 15.6 1.0
CE1 A:HIS764 4.5 10.9 1.0
HA A:ASP784 4.5 13.0 1.0
HD11 A:LEU757 4.6 13.9 1.0
HB A:ILE782 4.7 13.3 1.0
HG23 A:ILE782 4.7 15.6 1.0
H41 A:D6Z1001 4.7 14.1 1.0
CG A:HIS764 4.8 10.0 1.0
CB A:ALA783 4.8 10.1 1.0
C8 A:D6Z1001 4.8 11.7 1.0
HE2 A:PHE762 4.9 22.9 1.0
CB A:ILE782 4.9 11.1 1.0
O A:HOH1274 4.9 25.9 1.0
HB1 A:ALA783 4.9 12.2 1.0
HE1 A:HIS764 4.9 13.2 1.0
HB A:ILE685 5.0 16.4 1.0
HD12 A:ILE684 5.0 17.3 1.0
HD13 A:LEU679 5.0 19.2 1.0
CG A:ASP784 5.0 14.9 1.0

Fluorine binding site 2 out of 3 in 6fex

Go back to Fluorine Binding Sites List in 6fex
Fluorine binding site 2 out of 3 in the DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:16.4
occ:1.00
 F15 A:D6Z1001 0.0 16.4 1.0
C13 A:D6Z1001 1.3 14.5 1.0
F14 A:D6Z1001 2.1 14.4 1.0
F16 A:D6Z1001 2.2 16.7 1.0
C12 A:D6Z1001 2.3 14.9 1.0
H44 A:D6Z1001 2.6 17.9 1.0
H43 A:D6Z1001 2.6 17.9 1.0
HG23 A:ILE684 3.1 15.6 1.0
HD13 A:LEU679 3.2 19.2 1.0
HD11 A:LEU757 3.3 13.9 1.0
HD2 A:HIS764 3.3 11.2 1.0
HD11 A:LEU679 3.6 19.2 1.0
N11 A:D6Z1001 3.6 14.2 1.0
HD21 A:LEU757 3.7 15.2 1.0
HG21 A:ILE684 3.7 15.6 1.0
CG2 A:ILE684 3.8 13.0 1.0
HD12 A:ILE684 3.8 17.3 1.0
CD1 A:LEU679 3.8 16.0 1.0
HE2 A:PHE762 3.8 22.9 1.0
H42 A:D6Z1001 4.0 17.1 1.0
CD2 A:HIS764 4.0 9.3 1.0
HD13 A:LEU757 4.1 13.9 1.0
HG22 A:ILE782 4.1 15.6 1.0
CD1 A:LEU757 4.1 11.6 1.0
HG22 A:ILE684 4.1 15.6 1.0
HD12 A:LEU679 4.1 19.2 1.0
HE2 A:HIS764 4.3 11.9 1.0
HD22 A:LEU757 4.3 15.2 1.0
O A:ILE782 4.4 10.7 1.0
CD2 A:LEU757 4.4 12.6 1.0
CE2 A:PHE762 4.4 19.1 1.0
HA A:ALA783 4.5 10.1 1.0
NE2 A:HIS764 4.5 9.9 1.0
C9 A:D6Z1001 4.6 12.8 1.0
HB A:ILE782 4.7 13.3 1.0
CD1 A:ILE684 4.7 14.4 1.0
HB2 A:ASP784 4.7 13.7 1.0
HD12 A:LEU757 4.8 13.9 1.0
HG21 A:ILE782 4.8 15.6 1.0
O10 A:D6Z1001 4.8 13.1 1.0
CG2 A:ILE782 4.8 13.0 1.0
CG A:LEU757 4.9 11.3 1.0
HD22 A:LEU679 4.9 19.2 1.0
C A:ILE782 4.9 10.3 1.0
O A:ALA783 4.9 10.1 1.0
HD2 A:PHE762 5.0 19.4 1.0
HZ A:PHE762 5.0 23.1 1.0

Fluorine binding site 3 out of 3 in 6fex

Go back to Fluorine Binding Sites List in 6fex
Fluorine binding site 3 out of 3 in the DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, 2-[4-Bromo-2-Oxo-1'-(1H-Pyrazolo[4,3-B]Pyridine-5-Carbonyl) Spiro[Indole-3,4'-Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl) Acetamide, 1.291A, P212121, Rfree=17.4% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:16.7
occ:1.00
 F16 A:D6Z1001 0.0 16.7 1.0
C13 A:D6Z1001 1.3 14.5 1.0
F14 A:D6Z1001 2.1 14.4 1.0
F15 A:D6Z1001 2.2 16.4 1.0
C12 A:D6Z1001 2.3 14.9 1.0
H42 A:D6Z1001 2.6 17.1 1.0
H44 A:D6Z1001 2.7 17.9 1.0
N11 A:D6Z1001 2.8 14.2 1.0
HB2 A:ASP784 3.2 13.7 1.0
H43 A:D6Z1001 3.3 17.9 1.0
HE2 A:PHE762 3.3 22.9 1.0
O A:HOH1238 3.5 44.5 1.0
O A:HOH1274 3.6 25.9 1.0
HD2 A:HIS764 3.6 11.2 1.0
HB3 A:ASP784 3.6 13.7 1.0
HZ A:PHE762 3.8 23.1 1.0
CD2 A:HIS764 3.9 9.3 1.0
CB A:ASP784 3.9 11.4 1.0
HE2 A:HIS764 3.9 11.9 1.0
CE2 A:PHE762 4.0 19.1 1.0
C9 A:D6Z1001 4.0 12.8 1.0
NE2 A:HIS764 4.0 9.9 1.0
CZ A:PHE762 4.2 19.2 1.0
HD11 A:LEU679 4.2 19.2 1.0
HD13 A:LEU679 4.5 19.2 1.0
OD2 A:ASP784 4.6 18.6 1.0
O A:ALA783 4.6 10.1 1.0
O10 A:D6Z1001 4.7 13.1 1.0
HA A:HIS764 4.7 10.9 1.0
C A:ALA783 4.7 9.4 1.0
CG A:HIS764 4.7 10.0 1.0
CD1 A:LEU679 4.8 16.0 1.0
HA A:ALA783 4.8 10.1 1.0
CG A:ASP784 4.8 14.9 1.0
HD11 A:LEU757 4.8 13.9 1.0
N A:ASP784 4.8 9.4 1.0
H41 A:D6Z1001 4.9 14.1 1.0
HD12 A:LEU679 4.9 19.2 1.0
CE1 A:HIS764 4.9 10.9 1.0
HG22 A:ILE782 5.0 15.6 1.0
C8 A:D6Z1001 5.0 11.7 1.0
CA A:ASP784 5.0 10.8 1.0

Reference:

H.Richter, A.L.Satz, M.Bedoucha, B.Buettelmann, A.C.Petersen, A.Harmeier, R.Hermosilla, R.Hochstrasser, D.Burger, B.Gsell, R.Gasser, S.Huber, M.N.Hug, B.Kocer, B.Kuhn, M.Ritter, M.G.Rudolph, F.Weibel, J.Molina-David, J.J.Kim, J.V.Santos, M.Stihle, G.J.Georges, R.D.Bonfil, R.Fridman, S.Uhles, S.Moll, C.Faul, A.Fornoni, M.Prunotto. Dna-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in A Genetic Mouse Model of Alport Syndrome. Acs Chem.Biol. V. 14 37 2019.
ISSN: ESSN 1554-8937
PubMed: 30452219
DOI: 10.1021/ACSCHEMBIO.8B00866
Page generated: Thu Aug 1 20:07:29 2024

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