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Bromine 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
Iodine (I) 4 atoms
Chlorine (Cl) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total only one binding site of Bromine was 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:

Bromine binding site 1 out of 1 in 6fex

Go back to Bromine Binding Sites List in 6fex
Bromine binding site 1 out of 1 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 Bromine with other atoms in the Br 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:Br1001

b:14.7
occ:1.00
 BR1 A:D6Z1001 0.0 14.7 1.0
C2 A:D6Z1001 1.9 11.9 1.0
H45 A:D6Z1001 2.7 12.8 1.0
C3 A:D6Z1001 2.8 13.3 1.0
H52 A:D6Z1001 2.9 12.5 1.0
C36 A:D6Z1001 2.9 11.0 1.0
H37 A:D6Z1001 2.9 16.0 1.0
HB2 A:LYS655 3.0 14.9 1.0
HG22 A:THR701 3.0 19.6 1.0
HG13 A:VAL624 3.2 16.6 1.0
HB1 A:ALA653 3.4 16.7 1.0
HG21 A:THR701 3.4 19.6 1.0
C19 A:D6Z1001 3.5 9.9 1.0
C20 A:D6Z1001 3.5 10.6 1.0
HB3 A:ALA653 3.6 16.7 1.0
HG11 A:VAL624 3.6 16.6 1.0
C24 A:D6Z1001 3.7 10.4 1.0
H A:LYS655 3.7 13.4 1.0
CG2 A:THR701 3.7 16.3 1.0
CB A:LYS655 3.9 12.4 1.0
N A:LYS655 3.9 11.1 1.0
CG1 A:VAL624 3.9 13.8 1.0
CB A:ALA653 3.9 13.9 1.0
HB3 A:LYS655 4.0 14.9 1.0
O A:ALA653 4.0 13.1 1.0
C A:ALA653 4.1 11.7 1.0
C4 A:D6Z1001 4.1 14.4 1.0
H46 A:D6Z1001 4.1 12.8 1.0
C6 A:D6Z1001 4.2 11.9 1.0
HG23 A:THR701 4.2 19.6 1.0
HG22 A:VAL624 4.2 16.2 1.0
C A:VAL654 4.3 12.1 1.0
H51 A:D6Z1001 4.3 12.5 1.0
N A:VAL654 4.3 11.1 1.0
CA A:LYS655 4.3 10.5 1.0
N31 A:D6Z1001 4.4 12.4 1.0
HA A:VAL654 4.4 14.1 1.0
HG21 A:VAL624 4.5 16.2 1.0
HA A:LYS655 4.5 12.7 1.0
HG12 A:VAL624 4.5 16.6 1.0
N22 A:D6Z1001 4.6 11.3 1.0
CA A:VAL654 4.6 11.7 1.0
C21 A:D6Z1001 4.6 10.5 1.0
HD2 A:LYS655 4.6 16.1 1.0
H A:VAL654 4.6 13.4 1.0
O A:MET699 4.6 12.9 1.0
CA A:ALA653 4.7 12.6 1.0
C5 A:D6Z1001 4.7 13.1 1.0
H55 A:D6Z1001 4.7 18.9 1.0
CG2 A:VAL624 4.7 13.4 1.0
HB A:THR701 4.7 17.3 1.0
HB2 A:ALA653 4.7 16.7 1.0
C23 A:D6Z1001 4.8 11.2 1.0
CB A:THR701 4.8 14.4 1.0
C25 A:D6Z1001 4.9 12.4 1.0
O A:VAL654 4.9 12.4 1.0
H A:THR701 4.9 14.6 1.0
CB A:VAL624 4.9 13.0 1.0
C17 A:D6Z1001 4.9 11.1 1.0
H38 A:D6Z1001 5.0 17.4 1.0
H47 A:D6Z1001 5.0 12.6 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 Jul 11 01:53:56 2024

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