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Fluorine in PDB 6fiq: DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%

Enzymatic activity of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%

All present enzymatic activity of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%, PDB code: 6fiq 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) 46.23 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.934, 71.668, 72.644, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.8

Other elements in 6fiq:

The structure of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8% also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8% (pdb code 6fiq). 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, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%, PDB code: 6fiq:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6fiq

Go back to Fluorine Binding Sites List in 6fiq
Fluorine binding site 1 out of 3 in the DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:35.5
occ:1.00
 F13 A:DJW1001 0.0 35.5 1.0
C12 A:DJW1001 1.4 37.9 1.0
F14 A:DJW1001 2.2 36.6 1.0
F15 A:DJW1001 2.2 35.0 1.0
C11 A:DJW1001 2.5 35.3 1.0
N10 A:DJW1001 3.0 33.0 1.0
O19 A:DJW1001 3.0 31.4 1.0
C A:ALA777 3.0 28.6 1.0
CA A:ALA777 3.1 28.0 1.0
C9 A:DJW1001 3.2 32.4 1.0
O A:ALA777 3.3 30.2 1.0
N A:ASP778 3.5 28.2 1.0
O A:ILE776 3.5 29.6 1.0
N A:ALA777 3.8 28.1 1.0
C16 A:DJW1001 3.8 36.7 1.0
CB A:ASP778 3.8 30.2 1.0
C A:ILE776 3.9 30.6 1.0
NE2 A:HIS758 4.0 32.7 1.0
C18 A:DJW1001 4.1 36.5 1.0
CD2 A:HIS758 4.3 33.5 1.0
CA A:ASP778 4.3 31.3 1.0
CG2 A:ILE776 4.4 27.8 1.0
CB A:ALA777 4.4 30.2 1.0
C17 A:DJW1001 4.5 35.8 1.0
C8 A:DJW1001 4.5 31.8 1.0
CG2 A:ILE684 4.9 32.7 1.0

Fluorine binding site 2 out of 3 in 6fiq

Go back to Fluorine Binding Sites List in 6fiq
Fluorine binding site 2 out of 3 in the DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:36.6
occ:1.00
 F14 A:DJW1001 0.0 36.6 1.0
C12 A:DJW1001 1.4 37.9 1.0
F15 A:DJW1001 2.1 35.0 1.0
F13 A:DJW1001 2.2 35.5 1.0
C11 A:DJW1001 2.4 35.3 1.0
C16 A:DJW1001 3.0 36.7 1.0
N10 A:DJW1001 3.7 33.0 1.0
CD1 A:LEU679 3.8 37.9 1.0
CG2 A:ILE684 4.0 32.7 1.0
C17 A:DJW1001 4.2 35.8 1.0
CE1 A:PHE756 4.2 38.7 1.0
CD2 A:HIS758 4.2 33.5 1.0
CD1 A:LEU751 4.4 34.6 1.0
O19 A:DJW1001 4.4 31.4 1.0
CD2 A:LEU751 4.5 34.8 1.0
C18 A:DJW1001 4.5 36.5 1.0
C9 A:DJW1001 4.5 32.4 1.0
CZ A:PHE756 4.5 40.8 1.0
O A:ILE776 4.6 29.6 1.0
NE2 A:HIS758 4.7 32.7 1.0
CD1 A:PHE756 4.9 37.9 1.0
CG2 A:ILE776 5.0 27.8 1.0

Fluorine binding site 3 out of 3 in 6fiq

Go back to Fluorine Binding Sites List in 6fiq
Fluorine binding site 3 out of 3 in the DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, 1-(1H-Indazole-5-Carbonyl)-5'-Methoxy-1'-[2-Oxo-2-[(2S)-2- (Trifluoromethyl)Pyrrolidin-1-Yl]Ethyl]Spiro[Piperidine-4,3'- Pyrrolo[3,2-B]Pyridine]-2'-One, 1.790A, P212121, Rfree=23.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:35.0
occ:1.00
 F15 A:DJW1001 0.0 35.0 1.0
C12 A:DJW1001 1.3 37.9 1.0
F14 A:DJW1001 2.1 36.6 1.0
F13 A:DJW1001 2.2 35.5 1.0
C11 A:DJW1001 2.5 35.3 1.0
C16 A:DJW1001 2.9 36.7 1.0
N10 A:DJW1001 3.0 33.0 1.0
C17 A:DJW1001 3.2 35.8 1.0
C18 A:DJW1001 3.3 36.5 1.0
O A:HOH1150 3.4 40.5 1.0
CB A:ASP778 3.4 30.2 1.0
CD2 A:HIS758 3.5 33.5 1.0
NE2 A:HIS758 3.6 32.7 1.0
C9 A:DJW1001 4.0 32.4 1.0
CE1 A:PHE756 4.1 38.7 1.0
O A:ALA777 4.2 30.2 1.0
OD2 A:ASP778 4.2 41.2 1.0
CG A:ASP778 4.3 38.1 1.0
C A:ALA777 4.3 28.6 1.0
CZ A:PHE756 4.4 40.8 1.0
O19 A:DJW1001 4.4 31.4 1.0
CG A:HIS758 4.4 33.1 1.0
CE1 A:HIS758 4.5 32.2 1.0
N A:ASP778 4.5 28.2 1.0
CA A:ASP778 4.6 31.3 1.0
ND1 A:HIS758 4.9 35.0 1.0
CA A:ALA777 5.0 28.0 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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