Atomistry » Bromine » PDB 6e4l-6h45 » 6fex
Atomistry »
  Bromine »
    PDB 6e4l-6h45 »
      6fex »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy