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Iodine in PDB 5sb2: DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%

Enzymatic activity of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%

All present enzymatic activity of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%, PDB code: 5sb2 was solved by M.Stihle, H.Richter, J.Benz, B.Kocer, R.Hochstrasser, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.16, 68.462, 75.697, 90, 90, 90
R / Rfree (%) 20.7 / 23.2

Other elements in 5sb2:

The structure of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% (pdb code 5sb2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%, PDB code: 5sb2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 5sb2

Go back to Iodine Binding Sites List in 5sb2
Iodine binding site 1 out of 5 in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:31.7
occ:1.00
 N A:GLY780 3.5 30.5 1.0
NZ A:LYS655 3.7 42.7 1.0
N A:GLY619 3.7 41.4 1.0
O A:GLY622 3.8 41.3 1.0
CE A:LYS655 3.8 40.1 1.0
C A:GLU618 4.0 48.1 1.0
O A:HOH1247 4.0 48.5 1.0
CG2 A:VAL624 4.0 46.9 1.0
C A:GLY622 4.0 43.0 1.0
CA A:GLY780 4.1 26.5 1.0
CA A:GLY619 4.1 42.3 1.0
N A:GLU618 4.2 59.1 1.0
CD A:LYS655 4.2 32.4 1.0
CB A:PHE779 4.2 26.1 1.0
CA A:GLU623 4.2 52.9 1.0
CA A:GLU618 4.2 53.8 1.0
N A:GLU623 4.3 45.0 1.0
CD2 A:PHE779 4.5 27.9 1.0
O A:HOH1256 4.5 37.0 1.0
C A:GLY617 4.5 50.4 1.0
C A:PHE779 4.5 30.5 1.0
CA A:PHE779 4.6 29.7 1.0
O A:GLU618 4.6 36.8 1.0
C A:GLU623 4.6 51.1 1.0
N A:VAL624 4.6 48.0 1.0
O A:GLY617 4.7 46.9 1.0
CA A:GLY622 4.7 39.6 1.0
CG A:LYS655 4.8 32.1 1.0
CG A:PHE779 4.9 29.5 1.0

Iodine binding site 2 out of 5 in 5sb2

Go back to Iodine Binding Sites List in 5sb2
Iodine binding site 2 out of 5 in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:34.4
occ:1.00
 N A:GLN841 3.8 26.3 1.0
CA A:PHE839 3.8 21.7 1.0
C A:PHE839 3.9 23.5 1.0
CB A:GLN841 4.0 23.7 1.0
N A:GLY840 4.1 23.6 1.0
CG A:LEU842 4.2 26.9 1.0
O A:PHE839 4.3 22.7 1.0
CA A:GLN841 4.4 23.8 1.0
CG A:GLN841 4.4 23.6 1.0
N A:LEU842 4.5 26.9 1.0
CD1 A:LEU842 4.7 27.6 1.0
CD2 A:LEU842 4.7 29.1 1.0
C A:GLN841 4.7 27.4 1.0
N A:PHE839 4.7 22.0 1.0
CB A:PHE839 4.8 20.6 1.0
CD1 A:PHE839 4.8 23.5 1.0
C A:GLY840 4.9 27.1 1.0
O A:HOH1173 5.0 33.4 1.0
CA A:GLY840 5.0 28.7 1.0

Iodine binding site 3 out of 5 in 5sb2

Go back to Iodine Binding Sites List in 5sb2
Iodine binding site 3 out of 5 in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:53.3
occ:1.00
 O A:HOH1239 3.2 49.4 1.0
CA A:GLY617 3.9 47.3 1.0
C A:GLY617 4.0 50.4 1.0
CB A:GLU618 4.1 54.9 1.0
N A:GLY617 4.1 49.2 1.0
N A:GLU618 4.2 59.1 1.0
CG A:ARG783 4.2 27.5 1.0
CG A:LYS615 4.3 60.7 1.0
O A:HOH1240 4.3 38.9 1.0
CE A:LYS615 4.4 61.3 1.0
C A:LEU616 4.5 52.0 1.0
O A:GLY617 4.5 46.9 1.0
CA A:ARG783 4.7 28.8 1.0
O A:LEU616 4.7 43.5 1.0
CA A:GLU618 4.8 53.8 1.0
CB A:ARG783 4.8 28.3 1.0
CD A:LYS615 4.9 62.8 1.0
O A:HOH1292 4.9 42.0 1.0
CG A:GLU618 5.0 58.2 1.0

Iodine binding site 4 out of 5 in 5sb2

Go back to Iodine Binding Sites List in 5sb2
Iodine binding site 4 out of 5 in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:56.5
occ:1.00
 CD1 A:LEU877 3.2 42.1 1.0
NH1 A:ARG880 3.6 54.5 1.0
CG A:GLN894 3.7 37.9 1.0
NE2 A:GLN894 3.7 37.4 1.0
NE A:ARG880 3.9 55.9 1.0
CB A:PRO890 4.0 29.4 1.0
O A:GLN894 4.2 32.0 1.0
CD A:GLN894 4.2 45.1 1.0
CZ A:ARG880 4.2 55.8 1.0
CD2 A:LEU877 4.3 31.0 1.0
C A:GLN894 4.3 28.9 1.0
CG A:LEU877 4.3 33.4 1.0
CG A:PRO890 4.3 34.4 1.0
CB A:GLN894 4.4 30.0 1.0
CD2 A:LEU895 4.4 26.9 1.0
CB A:PHE898 4.4 26.8 1.0
N A:LEU895 4.5 26.8 1.0
CA A:LEU895 4.6 25.2 1.0
CD2 A:PHE898 4.6 33.1 1.0
CG A:PHE898 4.7 29.7 1.0
CB A:LEU877 4.9 33.2 1.0
CG A:LEU895 4.9 24.2 1.0
CA A:GLN894 5.0 26.1 1.0

Iodine binding site 5 out of 5 in 5sb2

Go back to Iodine Binding Sites List in 5sb2
Iodine binding site 5 out of 5 in the DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of DDR1, 3-Chloro-N-[(1R,2S)-2-Phenylcyclopropyl]-5-(1H-Pyrrolo[2,3- B]Pyridin-5-Yloxymethyl)Benzamide, 1.600A, P212121, Rfree=23.2% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:59.6
occ:1.00
 N A:LEU718 3.4 30.4 1.0
CA A:GLN717 3.6 32.3 1.0
CB A:GLN717 3.7 43.1 1.0
CG A:GLN717 3.9 44.4 1.0
C A:GLN717 4.0 33.4 1.0
O A:HOH1267 4.0 40.1 1.0
CD2 A:LEU833 4.3 35.4 1.0
CD1 A:LEU833 4.4 27.2 1.0
CB A:LEU718 4.4 28.9 1.0
CA A:LEU718 4.5 28.9 1.0
O A:HIS716 4.7 33.0 1.0
CG A:LEU833 4.7 28.8 1.0
CB A:LEU833 4.8 23.8 1.0
N A:GLN717 4.9 28.1 1.0
CZ A:ARG835 5.0 42.3 1.0
NH1 A:ARG835 5.0 41.7 1.0
NE A:ARG835 5.0 43.6 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Sun Aug 11 21:51:06 2024

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