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Iodine in PDB 6fil: DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%

Enzymatic activity of DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%

All present enzymatic activity of DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%, PDB code: 6fil 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) 47.83 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.042, 74.750, 75.080, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.5

Iodine Binding Sites:

The binding sites of Iodine atom in the DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5% (pdb code 6fil). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%, PDB code: 6fil:

Iodine binding site 1 out of 1 in 6fil

Go back to Iodine Binding Sites List in 6fil
Iodine binding site 1 out of 1 in the DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of DDR1, 2-[8-(1H-Indazole-5-Carbonyl)-4-Oxo-1-Phenyl-1,3,8- Triazaspiro[4.5]Decan-3-Yl]-N-Methylacetamide, 1.730A, P212121, Rfree=24.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:69.9
occ:1.00
 O A:HOH1347 3.3 43.4 1.0
O A:HOH1257 3.5 25.4 1.0
N A:GLN841 3.6 22.5 1.0
C A:PHE839 3.7 24.0 1.0
CB A:GLN841 3.8 24.3 1.0
CA A:PHE839 3.8 25.7 1.0
N A:GLY840 3.9 28.5 1.0
O A:PHE839 4.1 23.8 1.0
CA A:GLN841 4.1 24.5 1.0
CG A:LEU842 4.2 27.4 1.0
CG A:GLN841 4.2 40.7 1.0
N A:LEU842 4.4 25.1 1.0
O A:HOH1303 4.5 51.8 1.0
O A:HOH1147 4.6 32.3 1.0
C A:GLN841 4.6 27.7 1.0
N A:PHE839 4.6 20.7 1.0
C A:GLY840 4.6 29.2 1.0
CD1 A:LEU842 4.7 25.2 1.0
CA A:GLY840 4.8 27.9 1.0
CB A:PHE839 4.8 22.3 1.0
CD1 A:PHE839 4.9 25.8 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: Sun Aug 11 23:10:36 2024

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