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Fluorine in PDB 6fio: DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%

Enzymatic activity of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%

All present enzymatic activity of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%, PDB code: 6fio 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) 48.46 / 1.99
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 111.908, 111.908, 113.288, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 27.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7% (pdb code 6fio). 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-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%, PDB code: 6fio:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6fio

Go back to Fluorine Binding Sites List in 6fio
Fluorine binding site 1 out of 3 in the DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:40.2
occ:1.00
 F29 A:DJH1001 0.0 40.2 1.0
C28 A:DJH1001 1.3 41.1 1.0
F31 A:DJH1001 2.1 36.6 1.0
F30 A:DJH1001 2.2 42.9 1.0
C27 A:DJH1001 2.4 37.5 1.0
CG2 A:ILE684 3.6 34.1 1.0
N26 A:DJH1001 3.7 32.9 1.0
CD1 A:LEU679 3.8 42.0 1.0
O A:ILE776 4.1 41.5 1.0
CD2 A:HIS758 4.2 31.3 1.0
CD1 A:LEU751 4.3 42.4 1.0
CE1 A:PHE756 4.4 43.5 1.0
CD1 A:ILE684 4.5 31.5 1.0
CD2 A:LEU751 4.5 39.3 1.0
CG2 A:ILE776 4.5 35.5 1.0
O25 A:DJH1001 4.5 32.2 1.0
C24 A:DJH1001 4.6 32.3 1.0
NE2 A:HIS758 4.6 35.3 1.0
CZ A:PHE756 4.7 38.7 1.0
C A:ILE776 4.7 45.4 1.0
CB A:ILE684 4.9 38.1 1.0
O A:ALA777 4.9 43.5 1.0
CG A:LEU751 5.0 42.0 1.0

Fluorine binding site 2 out of 3 in 6fio

Go back to Fluorine Binding Sites List in 6fio
Fluorine binding site 2 out of 3 in the DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:42.9
occ:1.00
 F30 A:DJH1001 0.0 42.9 1.0
C28 A:DJH1001 1.3 41.1 1.0
F31 A:DJH1001 2.1 36.6 1.0
F29 A:DJH1001 2.2 40.2 1.0
C27 A:DJH1001 2.4 37.5 1.0
N26 A:DJH1001 2.9 32.9 1.0
O A:HOH1178 3.6 51.2 1.0
CZ A:PHE756 3.8 38.7 1.0
CE1 A:PHE756 3.8 43.5 1.0
CD2 A:HIS758 3.8 31.3 1.0
CB A:ASP778 3.9 46.0 1.0
NE2 A:HIS758 4.0 35.3 1.0
C24 A:DJH1001 4.0 32.3 1.0
OD2 A:ASP778 4.4 60.2 1.0
O25 A:DJH1001 4.6 32.2 1.0
CG A:ASP778 4.6 52.3 1.0
O A:ALA777 4.6 43.5 1.0
CD1 A:LEU679 4.6 42.0 1.0
C A:ALA777 4.8 42.3 1.0
CG A:HIS758 4.8 39.2 1.0
CE2 A:PHE756 5.0 39.9 1.0
N A:ASP778 5.0 37.2 1.0

Fluorine binding site 3 out of 3 in 6fio

Go back to Fluorine Binding Sites List in 6fio
Fluorine binding site 3 out of 3 in the DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, 2-[1'-(1H-Indazole-5-Carbonyl)-4-Methyl-2-Oxospiro[Indole-3,4'- Piperidine]-1-Yl]-N-(2,2,2-Trifluoroethyl)Acetamide, 1.990A, P6522, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:36.6
occ:1.00
 F31 A:DJH1001 0.0 36.6 1.0
C28 A:DJH1001 1.3 41.1 1.0
F30 A:DJH1001 2.1 42.9 1.0
F29 A:DJH1001 2.1 40.2 1.0
C27 A:DJH1001 2.4 37.5 1.0
N26 A:DJH1001 2.9 32.9 1.0
O A:ALA777 3.0 43.5 1.0
C A:ALA777 3.0 42.3 1.0
CA A:ALA777 3.3 41.5 1.0
C24 A:DJH1001 3.4 32.3 1.0
O25 A:DJH1001 3.4 32.2 1.0
NE2 A:HIS758 3.5 35.3 1.0
N A:ASP778 3.6 37.2 1.0
CB A:ASP778 3.6 46.0 1.0
O A:ILE776 3.6 41.5 1.0
N A:ALA777 3.8 38.6 1.0
CD2 A:HIS758 3.8 31.3 1.0
C A:ILE776 3.9 45.4 1.0
CG2 A:ILE776 4.0 35.5 1.0
CA A:ASP778 4.2 43.6 1.0
C23 A:DJH1001 4.6 37.2 1.0
CE1 A:HIS758 4.6 37.7 1.0
CB A:ALA777 4.7 41.1 1.0
CG A:ASP778 4.8 52.3 1.0
O A:HOH1178 4.8 51.2 1.0
CB A:ILE776 4.9 36.4 1.0
CA A:ILE776 5.0 37.1 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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