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Iodine in PDB 6fin: DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%

Enzymatic activity of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%

All present enzymatic activity of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%, PDB code: 6fin 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) 43.63 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.960, 62.120, 63.990, 90.00, 106.74, 90.00
R / Rfree (%) 19.8 / 22.8

Iodine Binding Sites:

The binding sites of Iodine atom in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% (pdb code 6fin). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%, PDB code: 6fin:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 1 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:35.5
occ:1.00
 CD A:LYS671 4.1 24.3 1.0
NZ A:LYS671 4.3 28.5 1.0
O A:HOH1248 4.4 30.2 1.0
CE A:LYS671 4.4 27.5 1.0
CD1 A:ILE675 4.7 35.9 1.0

Iodine binding site 2 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 2 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:57.6
occ:1.00
 N A:LEU718 3.5 34.7 1.0
CA A:GLN717 3.8 34.5 1.0
CB A:GLN717 3.9 39.9 1.0
CG A:GLN717 4.0 46.3 1.0
C A:GLN717 4.2 26.6 1.0
NH2 A:ARG841 4.2 40.8 0.6
CD2 A:LEU839 4.2 36.6 1.0
CD1 A:LEU839 4.4 29.6 1.0
CB A:LEU718 4.4 35.3 1.0
CZ A:ARG841 4.5 41.7 0.6
NE2 A:GLN717 4.5 53.0 1.0
CA A:LEU718 4.6 30.8 1.0
CG A:LEU839 4.7 39.9 1.0
NH1 A:ARG841 4.7 42.7 0.5
O A:HIS716 4.7 36.3 1.0
CD A:GLN717 4.8 49.2 1.0
CB A:LEU839 4.8 30.3 1.0
CZ A:ARG841 4.8 38.9 0.5
NE A:ARG841 4.8 34.5 0.6
NH2 A:ARG841 4.9 38.8 0.5
NH1 A:ARG841 4.9 34.0 0.6

Iodine binding site 3 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 3 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:57.3
occ:1.00
 NH2 A:ARG658 3.7 48.4 1.0
CG2 A:THR662 3.8 44.1 1.0
NH1 A:ARG658 3.8 49.9 1.0
N A:THR662 4.2 44.3 1.0
CD1 A:PHE621 4.2 40.7 1.0
CZ A:ARG658 4.2 50.2 1.0
CA A:ALA661 4.3 51.9 1.0
CE1 A:PHE621 4.5 42.3 1.0
O A:ASP660 4.6 47.0 1.0
C A:ALA661 4.7 41.5 1.0
CB A:ALA661 4.9 47.7 1.0
CB A:THR662 4.9 45.1 1.0
O A:HOH1116 4.9 42.3 1.0

Iodine binding site 4 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 4 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:60.6
occ:1.00
 CA A:GLY619 3.7 43.8 1.0
CE A:LYS655 3.9 40.7 1.0
C A:GLY622 3.9 51.7 1.0
O A:GLY622 3.9 45.0 1.0
CG2 A:VAL624 4.0 35.1 1.0
N A:GLY619 4.0 39.9 1.0
N A:GLU623 4.0 34.1 1.0
C A:GLU623 4.1 34.7 1.0
O A:HOH1182 4.1 44.2 1.0
CA A:GLU623 4.2 39.5 1.0
O A:HOH1154 4.2 44.4 1.0
O A:GLU623 4.3 34.5 1.0
CG A:LYS655 4.4 29.7 1.0
CD A:LYS655 4.4 36.6 1.0
N A:VAL624 4.4 32.9 1.0
CA A:GLY622 4.4 45.0 1.0
NZ A:LYS655 4.5 40.8 1.0
O A:HOH1283 4.6 37.1 1.0
N A:GLY622 4.7 45.1 1.0
C A:GLY619 4.8 50.7 1.0

Iodine binding site 5 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 5 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:41.1
occ:1.00
 O A:HOH1291 3.3 48.8 1.0
NH2 A:ARG886 3.7 34.0 1.0
NE A:ARG886 3.7 31.2 1.0
CB A:PRO896 4.0 28.2 1.0
CG A:PRO896 4.0 34.0 1.0
CD2 A:LEU901 4.1 24.9 1.0
CZ A:ARG886 4.2 36.9 1.0
CD1 A:LEU883 4.3 32.1 1.0
CG A:LEU883 4.3 29.4 1.0
O A:GLN900 4.4 26.0 1.0
CD2 A:PHE904 4.5 31.8 1.0
C A:GLN900 4.6 29.1 1.0
CB A:GLN900 4.6 29.1 1.0
CB A:PHE904 4.6 28.5 1.0
N A:LEU901 4.7 25.2 1.0
CA A:LEU901 4.8 25.8 1.0
CG A:LEU901 4.8 22.5 1.0
CG A:PHE904 4.9 28.4 1.0
CD A:ARG886 4.9 33.9 1.0
CB A:LEU883 4.9 27.7 1.0

Iodine binding site 6 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 6 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:1.0
occ:1.00
 C A:ASP681 3.7 35.3 1.0
N A:PRO682 3.8 34.3 1.0
O A:ASP681 3.9 31.0 1.0
O A:HOH1204 3.9 44.0 1.0
N A:ASP681 4.0 31.9 1.0
CA A:PRO682 4.1 33.0 1.0
CD A:ARG686 4.2 47.4 1.0
CA A:ASP681 4.2 34.0 1.0
CD A:PRO682 4.3 36.4 1.0
NH1 A:ARG686 4.3 55.6 1.0
CG A:PRO682 4.5 40.8 1.0
C A:LYS680 4.5 35.9 1.0
NE A:ARG686 4.7 53.8 1.0
CZ A:ARG686 4.8 56.9 1.0
CB A:PRO682 4.9 34.5 1.0

Iodine binding site 7 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 7 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:0.5
occ:1.00
 N A:SER739 3.5 30.7 1.0
OG A:SER739 3.9 34.1 1.0
CA A:ILE738 4.0 31.1 1.0
CB A:SER739 4.0 39.4 1.0
CB A:MET742 4.1 36.3 1.0
C A:ILE738 4.2 32.1 1.0
O A:THR737 4.4 38.0 1.0
CG1 A:ILE738 4.4 34.2 1.0
CG A:MET742 4.4 36.0 1.0
CA A:SER739 4.4 32.4 1.0
CE A:MET742 4.5 39.4 1.0
CZ A:PHE778 4.5 41.6 1.0
CE2 A:PHE778 4.7 39.6 1.0
CB A:ILE738 4.7 32.6 1.0
N A:ILE738 4.9 34.9 1.0
C A:THR737 5.0 38.0 1.0

Iodine binding site 8 out of 8 in 6fin

Go back to Iodine Binding Sites List in 6fin
Iodine binding site 8 out of 8 in the DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of DDR1, 3-[(3-Cyclopropyl-1,2,4-Oxadiazol-5-Yl)Methyl]-8-(1H-Indazole-5- Carbonyl)-1-Phenyl-1,3,8-Triazaspiro[4.5]Decan-4-One, 1.670A, P1211, Rfree=22.8% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:72.4
occ:1.00
 O A:GLY786 2.9 40.5 1.0
O A:HOH1117 3.0 37.6 1.0
NE A:ARG789 3.1 35.0 1.0
O A:HOH1131 3.2 39.8 1.0
NH2 A:ARG789 3.6 33.6 1.0
CB A:ARG789 3.7 33.1 1.0
N A:ARG789 3.7 30.8 1.0
CA A:MET787 3.8 34.1 1.0
CZ A:ARG789 3.8 33.0 1.0
C A:GLY786 3.9 36.6 1.0
C A:MET787 3.9 41.1 1.0
CG A:ARG789 4.0 30.8 1.0
N A:SER788 4.0 39.9 1.0
OH A:TYR796 4.1 26.6 1.0
CD A:ARG789 4.2 33.5 1.0
CE2 A:TYR796 4.2 26.7 1.0
N A:MET787 4.2 31.7 1.0
CA A:ARG789 4.3 27.7 1.0
CB A:PHE785 4.4 28.1 1.0
CB A:TYR792 4.4 24.3 1.0
CD2 A:TYR792 4.5 29.1 1.0
O A:HOH1170 4.5 46.8 1.0
O A:MET787 4.5 43.7 1.0
CZ A:TYR796 4.6 26.1 1.0
O A:ARG789 4.6 31.3 1.0
C A:SER788 4.7 47.4 1.0
CD A:ARG770 4.8 23.4 1.0
CG A:TYR792 4.9 25.8 1.0
CA A:SER788 4.9 45.2 1.0
C A:ARG789 4.9 33.6 1.0
C A:PHE785 5.0 30.6 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: Sun Aug 11 23:11:02 2024

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