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Chlorine 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:

Fluorine (F) 3 atoms
Bromine (Br) 1 atom
Iodine (I) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6fex

Go back to Chlorine Binding Sites List in 6fex
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1007

b:30.6
occ:1.00
 H A:SER739 2.7 20.8 1.0
HA A:ILE738 3.1 22.1 1.0
HG13 A:ILE738 3.4 21.7 1.0
HB2 A:MET742 3.4 19.9 1.0
N A:SER739 3.5 17.3 1.0
HG2 A:MET742 3.5 23.9 1.0
O A:HOH1317 3.5 37.2 1.0
HB3 A:SER739 3.6 21.8 1.0
HE3 A:MET742 3.8 31.8 1.0
OG A:SER739 3.8 19.5 1.0
HB3 A:MET742 3.8 19.9 1.0
HE2 A:MET742 3.8 31.8 1.0
CA A:ILE738 3.9 18.4 1.0
CB A:MET742 4.0 16.6 1.0
HG A:SER739 4.0 23.4 1.0
CB A:SER739 4.1 18.1 1.0
HZ A:PHE778 4.2 35.1 1.0
CG A:MET742 4.2 19.9 1.0
C A:ILE738 4.2 18.1 1.0
CG1 A:ILE738 4.2 18.0 1.0
CE A:MET742 4.2 26.5 1.0
HG12 A:ILE738 4.4 21.7 1.0
CA A:SER739 4.4 16.9 1.0
CZ A:PHE778 4.5 29.2 1.0
O A:THR737 4.5 23.4 1.0
HE1 A:PHE778 4.6 35.2 1.0
CB A:ILE738 4.7 18.4 1.0
CE1 A:PHE778 4.7 29.3 1.0
HB A:ILE738 4.9 22.1 1.0
HG3 A:MET742 4.9 23.9 1.0
N A:ILE738 5.0 21.0 1.0
HB2 A:SER739 5.0 21.8 1.0

Chlorine binding site 2 out of 4 in 6fex

Go back to Chlorine Binding Sites List in 6fex
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1008

b:29.7
occ:1.00
 HH11 A:ARG686 1.8 37.4 0.5
NH1 A:ARG686 2.5 31.1 0.5
O A:HOH1188 2.7 41.4 1.0
HH12 A:ARG686 2.8 37.4 0.5
HD2 A:ARG686 3.0 32.4 0.5
HD3 A:ARG686 3.1 34.3 0.5
HH11 A:ARG686 3.3 39.9 0.5
HD3 A:ARG686 3.3 32.4 0.5
HA A:PRO682 3.4 18.3 1.0
CD A:ARG686 3.6 26.9 0.5
C A:ASP681 3.6 13.1 1.0
N A:PRO682 3.7 13.8 1.0
CZ A:ARG686 3.7 30.9 0.5
HD3 A:PRO682 3.7 20.2 1.0
NH1 A:ARG686 3.8 33.2 0.5
O A:ASP681 3.9 13.4 1.0
HG3 A:PRO682 3.9 22.8 1.0
HA A:ASP681 3.9 15.8 1.0
N A:ASP681 3.9 14.2 1.0
H A:ASP681 4.0 17.0 1.0
CA A:PRO682 4.0 15.2 1.0
CD A:ARG686 4.0 28.6 0.5
CA A:ASP681 4.0 13.2 1.0
NE A:ARG686 4.1 29.5 0.5
CD A:PRO682 4.1 16.8 1.0
HH12 A:ARG686 4.2 39.9 0.5
O A:HOH1129 4.3 20.6 1.0
C A:LYS680 4.3 15.4 1.0
CG A:PRO682 4.4 19.0 1.0
HA A:LYS680 4.4 18.6 1.0
HB2 A:ARG686 4.5 24.5 0.5
CZ A:ARG686 4.5 33.1 0.5
HB2 A:ARG686 4.5 25.3 0.5
HD2 A:ARG686 4.5 34.3 0.5
NE A:ARG686 4.5 31.6 0.5
HB3 A:PRO682 4.6 20.9 1.0
CB A:PRO682 4.7 17.4 1.0
HG3 A:ARG686 4.7 30.1 0.5
O A:LYS680 4.7 17.0 1.0
HB3 A:LYS680 4.8 22.5 1.0
NH2 A:ARG686 4.8 32.4 0.5
CG A:ARG686 4.8 25.1 0.5
CA A:LYS680 4.9 15.5 1.0
HH22 A:ARG686 4.9 38.9 0.5
HE A:ARG686 4.9 35.4 0.5
CG A:ARG686 4.9 23.8 0.5

Chlorine binding site 3 out of 4 in 6fex

Go back to Chlorine Binding Sites List in 6fex
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1009

b:32.5
occ:1.00
 SG A:CYS698 3.2 16.3 0.5
HH11 A:ARG607 3.3 26.6 1.0
HD13 A:ILE656 3.4 20.8 1.0
HG12 A:ILE656 3.5 19.0 1.0
HG2 A:PRO696 3.5 24.4 1.0
HG3 A:ARG607 3.6 31.6 1.0
HD11 A:ILE656 3.7 20.8 1.0
HG A:CYS698 3.7 19.6 0.5
HG11 A:VAL654 3.9 17.4 1.0
CD1 A:ILE656 3.9 17.3 1.0
O A:HOH1319 3.9 36.8 1.0
HD12 A:LEU610 3.9 19.4 1.0
HH12 A:ARG607 3.9 26.6 1.0
NH1 A:ARG607 4.0 22.1 1.0
HB3 A:CYS698 4.1 20.3 0.5
HG21 A:ILE656 4.2 16.7 1.0
CG1 A:ILE656 4.2 15.8 1.0
HD13 A:LEU610 4.2 19.4 1.0
HG23 A:ILE656 4.2 16.7 1.0
HG2 A:ARG607 4.3 31.6 1.0
HG3 A:PRO696 4.3 24.4 1.0
CG A:PRO696 4.4 20.3 1.0
CG A:ARG607 4.4 26.3 1.0
SG A:CYS698 4.4 18.4 0.5
CD1 A:LEU610 4.5 16.1 1.0
HD3 A:ARG607 4.6 31.1 1.0
CB A:CYS698 4.6 16.9 0.5
CG2 A:ILE656 4.6 13.9 1.0
O A:HOH1427 4.6 36.8 1.0
HG12 A:VAL654 4.6 17.4 1.0
HB2 A:CYS698 4.7 20.3 0.5
HB2 A:LEU610 4.7 20.3 1.0
HD2 A:PRO696 4.7 22.4 1.0
O A:HOH1235 4.7 50.0 1.0
CG1 A:VAL654 4.7 14.5 1.0
HB3 A:CYS698 4.7 18.2 0.5
CB A:CYS698 4.7 15.1 0.5
HD12 A:ILE656 4.8 20.8 1.0
HG13 A:ILE656 4.8 19.0 1.0

Chlorine binding site 4 out of 4 in 6fex

Go back to Chlorine Binding Sites List in 6fex
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1010

b:27.5
occ:1.00
 O A:HOH1378 2.3 33.6 1.0
H A:LEU718 2.4 23.4 1.0
HA A:GLN717 2.7 25.9 1.0
HB3 A:GLN717 2.9 32.5 1.0
HG A:LEU839 3.0 19.0 1.0
HG2 A:GLN717 3.2 40.3 1.0
N A:LEU718 3.2 19.4 1.0
CA A:GLN717 3.4 21.6 1.0
CB A:GLN717 3.4 27.1 1.0
C A:GLN717 3.8 19.6 1.0
CG A:GLN717 3.8 33.5 1.0
O A:HOH1158 3.9 25.3 1.0
HB3 A:LEU718 3.9 24.0 1.0
CG A:LEU839 4.0 15.8 1.0
O A:HOH1298 4.0 22.6 1.0
HB2 A:LEU718 4.0 24.0 1.0
HD23 A:LEU839 4.0 20.2 1.0
HD2 A:ARG841 4.2 20.2 0.5
HB2 A:LEU839 4.2 16.2 1.0
HD21 A:LEU839 4.3 20.2 1.0
CB A:LEU718 4.3 20.0 1.0
CD2 A:LEU839 4.3 16.8 1.0
HB2 A:GLN717 4.3 32.5 1.0
HD3 A:ARG841 4.3 23.6 0.5
CA A:LEU718 4.4 18.9 1.0
HG3 A:GLN717 4.5 40.3 1.0
HE A:ARG841 4.5 25.4 0.5
O A:HIS716 4.6 20.6 1.0
NE A:ARG841 4.6 21.1 0.5
HH11 A:ARG841 4.6 29.1 0.5
CB A:LEU839 4.7 13.5 1.0
N A:GLN717 4.7 19.7 1.0
HD11 A:LEU839 4.8 20.0 1.0
NH1 A:ARG841 4.8 24.2 0.5
HB3 A:LEU839 4.9 16.2 1.0
CD A:ARG841 4.9 19.6 0.5
CD1 A:LEU839 4.9 16.7 1.0
OE1 A:GLN717 4.9 38.9 1.0
CD A:GLN717 4.9 37.8 1.0
CZ A:ARG841 4.9 23.4 0.5
CD A:ARG841 4.9 16.8 0.5
HD12 A:LEU839 5.0 20.0 1.0
HD3 A:ARG841 5.0 20.2 0.5
HD2 A:ARG841 5.0 23.6 0.5

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: Sat Jul 27 23:13:41 2024

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