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Iodine 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
Chlorine (Cl) 4 atoms

Iodine Binding Sites:

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

Iodine binding site 1 out of 4 in 6fex

Go back to Iodine Binding Sites List in 6fex
Iodine 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 Iodine with other atoms in the I 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:I1002

b:18.5
occ:1.00
 HE A:ARG886 2.8 18.7 1.0
HH21 A:ARG886 2.9 19.4 1.0
O A:HOH1284 3.2 33.7 1.0
HD23 A:LEU901 3.3 15.6 1.0
HG3 A:GLN900 3.3 22.6 1.0
O A:HOH1400 3.4 41.1 1.0
HB3 A:PRO896 3.4 17.5 1.0
HD12 A:LEU883 3.5 17.3 1.0
NE A:ARG886 3.6 15.6 1.0
HG A:LEU883 3.6 13.9 1.0
NH2 A:ARG886 3.7 16.1 1.0
HG3 A:PRO896 3.8 17.3 1.0
HG2 A:PRO896 3.8 17.3 1.0
HA A:LEU901 3.9 11.0 1.0
HB2 A:PRO896 3.9 17.5 1.0
HD2 A:PHE904 3.9 14.4 1.0
HB3 A:GLN900 3.9 16.2 1.0
HB2 A:PHE904 3.9 12.6 1.0
HG2 A:GLN900 3.9 22.6 1.0
CB A:PRO896 3.9 14.6 1.0
CG A:GLN900 4.0 18.8 1.0
CG A:PRO896 4.1 14.4 1.0
CZ A:ARG886 4.1 16.2 1.0
HD21 A:LEU901 4.1 15.6 1.0
CD2 A:LEU901 4.1 12.9 1.0
CD1 A:LEU883 4.2 14.4 1.0
HD11 A:LEU883 4.2 17.3 1.0
CG A:LEU883 4.3 11.6 1.0
HH22 A:ARG886 4.4 19.4 1.0
HG A:LEU901 4.4 13.1 1.0
CD2 A:PHE904 4.4 12.0 1.0
O A:GLN900 4.4 11.1 1.0
CB A:GLN900 4.5 13.4 1.0
C A:GLN900 4.5 10.5 1.0
HB2 A:LEU883 4.5 15.1 1.0
HD2 A:ARG886 4.5 17.7 1.0
HA A:LEU883 4.6 13.5 1.0
HB3 A:PHE904 4.6 12.6 1.0
N A:LEU901 4.6 10.2 1.0
CB A:PHE904 4.6 10.5 1.0
CA A:LEU901 4.6 9.2 1.0
CD A:ARG886 4.7 14.7 1.0
CG A:PHE904 4.8 11.2 1.0
CG A:LEU901 4.8 10.9 1.0
HH21 A:ARG903 4.8 17.1 1.0
HD22 A:LEU901 4.9 15.6 1.0
CB A:LEU883 4.9 12.5 1.0
H A:LEU901 4.9 12.2 1.0
HB2 A:ARG886 5.0 13.2 1.0

Iodine binding site 2 out of 4 in 6fex

Go back to Iodine Binding Sites List in 6fex
Iodine 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 Iodine with other atoms in the I 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:I1003

b:25.2
occ:1.00
 HA3 A:GLY619 2.9 17.2 1.0
O A:HOH1361 2.9 39.0 1.0
HE3 A:LYS655 3.1 18.9 1.0
HG23 A:VAL624 3.3 16.2 1.0
O A:HOH1278 3.4 21.2 1.0
O A:HOH1385 3.5 37.7 1.0
HG3 A:LYS655 3.7 15.7 1.0
O A:HOH1308 3.8 33.4 1.0
CA A:GLY619 3.8 14.3 1.0
C A:GLY622 3.8 13.0 1.0
HA A:GLU623 3.8 16.7 1.0
O A:HOH1265 3.8 19.6 1.0
H A:GLY619 3.9 19.4 1.0
O A:GLY622 3.9 13.5 1.0
N A:GLU623 3.9 12.7 1.0
N A:GLY619 4.1 16.1 1.0
HA3 A:GLY622 4.1 16.9 1.0
CE A:LYS655 4.1 15.8 1.0
CG2 A:VAL624 4.1 13.4 1.0
HG22 A:VAL624 4.2 16.2 1.0
H A:GLU623 4.2 15.3 1.0
CA A:GLU623 4.2 13.9 1.0
C A:GLU623 4.2 12.8 1.0
HA2 A:GLY619 4.2 17.2 1.0
H A:GLY622 4.2 14.5 1.0
CA A:GLY622 4.4 14.1 1.0
O A:GLU623 4.4 13.1 1.0
HG21 A:VAL624 4.4 16.2 1.0
HE2 A:LYS655 4.4 18.9 1.0
O A:HOH1409 4.5 19.2 1.0
CG A:LYS655 4.5 13.1 1.0
N A:GLY622 4.6 12.1 1.0
N A:VAL624 4.7 11.8 1.0
O A:HOH1214 4.7 31.6 1.0
CD A:LYS655 4.8 13.4 1.0
HD2 A:LYS655 4.8 16.1 1.0
H A:VAL624 4.8 14.2 1.0
C A:GLY619 4.8 13.3 1.0
HZ1 A:LYS655 4.8 20.8 1.0
HG2 A:LYS655 4.9 15.7 1.0
HZ2 A:LYS655 4.9 20.8 1.0
NZ A:LYS655 4.9 17.3 1.0
O A:HOH1224 4.9 27.1 1.0
C A:GLU618 5.0 17.4 1.0

Iodine binding site 3 out of 4 in 6fex

Go back to Iodine Binding Sites List in 6fex
Iodine 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 Iodine with other atoms in the I 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:I1004

b:20.8
occ:1.00
 HH22 A:ARG658 2.6 20.5 1.0
HH12 A:ARG658 2.9 23.5 1.0
HG23 A:THR662 3.0 23.6 1.0
HA A:ALA661 3.2 22.3 1.0
H A:THR662 3.4 20.1 1.0
NH2 A:ARG658 3.5 17.0 1.0
HD1 A:PHE621 3.5 18.4 1.0
HE1 A:PHE621 3.6 19.8 1.0
NH1 A:ARG658 3.7 19.5 1.0
CG2 A:THR662 3.9 19.6 1.0
HG22 A:THR662 4.0 23.6 1.0
N A:THR662 4.0 16.7 1.0
CZ A:ARG658 4.0 18.8 1.0
CA A:ALA661 4.1 18.6 1.0
HH21 A:ARG658 4.1 20.5 1.0
O A:ASP660 4.1 20.2 1.0
CD1 A:PHE621 4.2 15.3 1.0
CE1 A:PHE621 4.3 16.4 1.0
HG21 A:THR662 4.3 23.6 1.0
HH11 A:ARG658 4.4 23.5 1.0
C A:ALA661 4.5 17.3 1.0
HB1 A:ALA661 4.7 21.6 1.0
O A:HOH1432 4.8 54.3 1.0
C A:ASP660 4.9 19.3 1.0
CB A:ALA661 4.9 18.0 1.0
N A:ALA661 4.9 17.9 1.0
CA A:THR662 4.9 17.4 1.0
CB A:THR662 4.9 18.9 1.0

Iodine binding site 4 out of 4 in 6fex

Go back to Iodine Binding Sites List in 6fex
Iodine 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 Iodine with other atoms in the I 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:I1005

b:29.9
occ:1.00
 O1S A:MES1006 2.4 17.1 1.0
H81 A:MES1006 2.7 26.7 1.0
H A:GLN847 2.9 13.5 1.0
HA A:PHE845 3.0 10.4 1.0
HB2 A:GLN847 3.1 15.6 0.5
HB2 A:GLN847 3.1 16.1 0.5
O A:HOH1255 3.1 11.3 1.0
HG A:LEU848 3.2 16.7 1.0
C8 A:MES1006 3.3 22.2 1.0
H82 A:MES1006 3.3 26.7 1.0
S A:MES1006 3.4 16.7 1.0
HG3 A:GLN847 3.7 16.7 0.5
N A:GLN847 3.7 11.2 1.0
C A:PHE845 3.8 9.9 1.0
CA A:PHE845 3.8 8.7 1.0
O3S A:MES1006 3.9 16.4 1.0
HD1 A:PHE845 3.9 12.4 1.0
HG2 A:GLN847 3.9 17.7 0.5
CB A:GLN847 3.9 13.0 0.5
CB A:GLN847 3.9 13.4 0.5
H A:GLY846 4.0 13.1 1.0
N A:GLY846 4.0 10.9 1.0
H A:LEU848 4.0 13.6 1.0
H51 A:MES1006 4.1 36.4 1.0
CG A:LEU848 4.1 13.9 1.0
O A:PHE845 4.2 10.5 1.0
CA A:GLN847 4.3 11.5 0.5
CA A:GLN847 4.3 11.7 0.5
CG A:GLN847 4.3 13.9 0.5
CG A:GLN847 4.3 14.7 0.5
HD11 A:LEU848 4.4 18.2 1.0
N A:LEU848 4.4 11.3 1.0
HD21 A:LEU848 4.5 17.4 1.0
HG3 A:GLN847 4.5 17.7 0.5
HB3 A:PHE845 4.5 11.1 1.0
O2S A:MES1006 4.6 13.9 1.0
OE1 A:GLN847 4.6 14.7 0.5
H A:PHE845 4.6 11.5 1.0
HD12 A:LEU848 4.6 18.2 1.0
C A:GLN847 4.6 12.1 1.0
CD1 A:LEU848 4.7 15.1 1.0
HB3 A:GLN847 4.7 15.6 0.5
HB3 A:GLN847 4.7 16.1 0.5
HD23 A:LEU848 4.7 17.4 1.0
CD2 A:LEU848 4.7 14.5 1.0
N A:PHE845 4.7 9.6 1.0
CB A:PHE845 4.7 9.3 1.0
CD1 A:PHE845 4.7 10.3 1.0
C7 A:MES1006 4.7 27.3 1.0
C A:GLY846 4.8 12.6 1.0
HN4 A:MES1006 4.8 36.4 1.0
CD A:GLN847 4.9 15.2 0.5
CA A:GLY846 4.9 11.4 1.0
HB2 A:LEU848 5.0 14.6 1.0
O A:HOH1113 5.0 29.2 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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