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Iodine in PDB 5m0d: Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

Enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

All present enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors:
3.1.4.39;

Protein crystallography data

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0d was solved by W.-J.Keune, T.Heidebrecht, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.34 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.927, 88.012, 77.356, 90.00, 103.10, 90.00
R / Rfree (%) 22.5 / 27

Other elements in 5m0d:

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5m0d

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Iodine binding site 1 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I909

b:64.0
occ:1.00
 N A:ASN230 3.7 43.6 1.0
NH1 A:ARG391 3.7 46.5 1.0
CA A:GLY229 3.9 42.7 1.0
N A:SER231 4.0 45.9 1.0
CE A:LYS208 4.1 46.0 1.0
O A:SER231 4.1 46.0 1.0
C A:GLY229 4.2 43.2 1.0
CG A:LYS208 4.3 44.3 1.0
CD1 A:LEU389 4.3 46.0 1.0
CG1 A:VAL385 4.3 48.7 1.0
CD2 A:LEU389 4.3 46.0 1.0
CA A:ASN230 4.5 44.4 1.0
CB A:ASN230 4.5 44.7 1.0
OG A:SER231 4.6 48.2 1.0
CD A:LYS208 4.6 45.2 1.0
CG A:LEU389 4.7 46.5 1.0
CB A:SER231 4.7 48.0 1.0
C A:ASN230 4.8 45.5 1.0
CA A:SER231 4.8 47.0 1.0
CZ A:ARG391 4.8 47.0 1.0
C A:SER231 4.9 46.6 1.0

Iodine binding site 2 out of 9 in 5m0d

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Iodine binding site 2 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:79.3
occ:0.79
 C A:MET232 3.8 48.1 1.0
NH2 A:ARG393 3.8 58.7 1.0
N A:TYR233 3.9 48.4 1.0
N A:MET232 4.0 47.1 1.0
CA A:MET232 4.0 47.0 1.0
O A:MET232 4.1 48.7 1.0
CE1 A:HIS242 4.1 58.3 1.0
CB A:TYR233 4.2 50.5 1.0
CG2 A:VAL385 4.5 49.6 1.0
CA A:TYR233 4.5 49.5 1.0
C A:SER231 4.5 46.6 1.0
OG A:SER240 4.5 56.8 1.0
CB A:SER240 4.6 56.0 1.0
CB A:SER231 4.6 48.0 1.0
NE2 A:HIS242 4.7 59.2 1.0
ND1 A:HIS242 4.9 57.5 1.0
O A:SER231 5.0 46.0 1.0

Iodine binding site 3 out of 9 in 5m0d

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Iodine binding site 3 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I911

b:0.8
occ:0.79
 O A:CYS566 3.7 79.3 1.0
O A:PHE562 3.9 85.4 1.0
CG A:PRO654 3.9 79.5 1.0
N A:LEU564 4.0 78.9 1.0
CB A:CYS566 4.0 74.6 1.0
CB A:PRO654 4.1 77.9 1.0
CB A:PHE562 4.1 82.4 1.0
N A:CYS566 4.1 76.7 1.0
CD A:PRO654 4.3 79.0 1.0
C A:PHE562 4.3 84.2 1.0
CA A:CYS566 4.4 76.2 1.0
C A:CYS566 4.5 78.0 1.0
CA A:ASP563 4.5 83.0 1.0
CB A:LEU564 4.5 75.3 1.0
CG A:LEU564 4.7 75.3 1.0
CA A:LEU564 4.8 76.7 1.0
SG A:CYS566 4.8 72.4 1.0
C A:ASP563 4.8 80.6 1.0
N A:ASP563 4.8 83.4 1.0
N A:GLY565 4.8 77.7 1.0
CD1 A:LEU564 4.9 74.3 1.0
CA A:PHE562 4.9 83.5 1.0
N A:PRO654 5.0 77.0 1.0

Iodine binding site 4 out of 9 in 5m0d

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Iodine binding site 4 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I912

b:0.5
occ:0.73
 OG1 A:THR334 3.0 52.9 1.0
OG A:SER307 3.2 55.5 1.0
ND1 A:HIS281 3.3 56.8 1.0
CB A:THR334 3.7 52.5 1.0
CE1 A:HIS281 3.7 56.2 1.0
CG A:HIS281 3.9 56.5 1.0
CA A:ILE331 3.9 54.2 1.0
CG1 A:ILE331 4.0 52.9 1.0
CG2 A:THR334 4.1 52.1 1.0
CB A:SER307 4.1 54.6 1.0
N A:ILE331 4.2 55.8 1.0
O A:GLU330 4.3 57.5 1.0
CB A:HIS281 4.3 57.0 1.0
NE2 A:HIS281 4.4 55.7 1.0
C A:GLU330 4.4 57.5 1.0
CD2 A:HIS281 4.5 55.8 1.0
CB A:ILE331 4.5 53.2 1.0
CZ A:PHE305 4.7 54.0 1.0
CE2 A:PHE305 4.7 53.3 1.0
O A:ILE331 4.9 53.7 1.0
C A:ILE331 4.9 54.1 1.0

Iodine binding site 5 out of 9 in 5m0d

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Iodine binding site 5 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I913

b:0.4
occ:0.57
 OE1 A:GLU847 3.3 54.9 1.0
CG A:GLU847 3.7 52.8 1.0
CD A:GLU847 3.8 54.5 1.0
O A:GLU847 3.8 49.4 1.0
N A:LEU788 3.9 59.1 1.0
NH1 A:ARG843 4.0 57.5 1.0
CG A:ARG843 4.0 56.4 1.0
CD2 A:LEU851 4.1 48.5 1.0
CD1 A:ILE848 4.1 51.4 1.0
CB A:LEU788 4.2 57.4 1.0
CB A:LEU851 4.3 46.9 1.0
C A:GLU847 4.3 50.0 1.0
CB A:ARG843 4.4 56.0 1.0
O A:LEU788 4.4 55.9 1.0
CD1 A:LEU851 4.5 47.8 1.0
CG A:LEU851 4.5 47.4 1.0
CA A:LEU788 4.5 58.0 1.0
CB A:GLU847 4.6 52.5 1.0
CA A:PRO787 4.6 62.0 1.0
CB A:PRO787 4.7 61.1 1.0
N A:ILE848 4.7 50.0 1.0
OE2 A:GLU847 4.7 55.8 1.0
CG A:LEU788 4.8 58.5 1.0
C A:PRO787 4.8 61.0 1.0
CA A:ILE848 4.9 49.2 1.0
CD A:ARG843 5.0 58.2 1.0
C A:LEU788 5.0 56.5 1.0

Iodine binding site 6 out of 9 in 5m0d

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Iodine binding site 6 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I914

b:0.8
occ:0.71
 OD1 A:ASP782 3.4 78.7 1.0
N A:ALA781 3.8 74.6 1.0
CA A:SER636 3.9 70.5 1.0
N A:ASP782 3.9 74.7 1.0
CG A:ASP782 3.9 78.5 1.0
CB A:ALA781 4.0 72.0 1.0
CB A:PRO780 4.0 79.6 1.0
CB A:SER636 4.3 72.8 1.0
O A:ASN728 4.3 67.7 1.0
CG2 A:THR634 4.3 61.1 1.0
CA A:ALA781 4.3 72.9 1.0
CA A:GLY729 4.4 65.5 1.0
N A:SER636 4.4 68.7 1.0
O A:ILE635 4.4 65.0 1.0
CB A:ASP782 4.4 76.5 1.0
OD2 A:ASP782 4.5 79.8 1.0
C A:PRO780 4.6 76.0 1.0
C A:ILE635 4.6 66.0 1.0
C A:ALA781 4.7 73.2 1.0
CA A:PRO780 4.8 77.8 1.0
CA A:ASP782 4.8 75.3 1.0
C A:GLY729 5.0 63.0 1.0

Iodine binding site 7 out of 9 in 5m0d

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Iodine binding site 7 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:84.3
occ:0.47
 N A:SER846 3.7 51.6 1.0
CB A:SER846 3.8 51.2 1.0
CD A:PRO541 3.9 57.4 1.0
OG A:SER846 4.0 52.1 1.0
N A:TYR845 4.1 53.9 1.0
CG A:PRO541 4.2 56.3 1.0
CA A:SER846 4.4 50.6 1.0
CB A:TYR845 4.4 53.2 1.0
C A:TYR845 4.5 51.4 1.0
CA A:TYR845 4.5 52.7 1.0
CB A:SER844 4.7 55.8 1.0
C A:SER844 4.9 54.1 1.0

Iodine binding site 8 out of 9 in 5m0d

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Iodine binding site 8 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:92.3
occ:0.56
 NH1 A:ARG746 3.7 49.9 1.0
N A:GLU749 3.9 57.1 1.0
CA A:THR748 4.1 53.4 1.0
CE1 A:PHE625 4.3 51.1 1.0
CB A:THR748 4.4 54.1 1.0
CG A:GLU749 4.5 60.8 1.0
C A:THR748 4.5 54.9 1.0
CZ A:PHE625 4.6 50.5 1.0
CE2 A:TYR605 4.6 51.6 1.0
CD2 A:TYR605 4.7 51.9 1.0
CG2 A:THR748 4.7 53.6 1.0
OE1 A:GLU749 4.7 63.3 1.0
CB A:GLU749 4.9 60.3 1.0
CZ A:ARG746 5.0 49.1 1.0
CA A:GLU749 5.0 58.8 1.0
O A:ASP747 5.0 50.0 1.0

Iodine binding site 9 out of 9 in 5m0d

Go back to Iodine Binding Sites List in 5m0d
Iodine binding site 9 out of 9 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:81.6
occ:0.81
 CD1 A:LEU458 3.8 82.8 1.0
CG A:LEU458 3.9 80.8 1.0
CD A:PRO457 4.0 74.7 1.0
N A:LEU458 4.1 75.6 1.0
CB A:LEU458 4.3 78.2 1.0
N A:PRO457 4.3 73.2 1.0
CB A:PRO457 4.4 76.3 1.0
CD A:LYS456 4.4 74.3 1.0
CG A:PRO457 4.5 75.9 1.0
CB A:LYS456 4.6 72.1 1.0
CA A:PRO457 4.7 74.0 1.0
C A:PRO457 4.8 74.8 1.0
CG A:LYS456 4.8 72.1 1.0
CA A:LEU458 4.9 76.0 1.0
C A:LYS456 5.0 71.2 1.0

Reference:

W.J.Keune, F.Potjewyd, T.Heidebrecht, F.Salgado-Polo, S.J.Macdonald, L.Chelvarajan, A.Abdel Latif, S.Soman, A.J.Morris, A.J.Watson, C.Jamieson, A.Perrakis. Rational Design of Autotaxin Inhibitors By Structural Evolution of Endogenous Modulators. J. Med. Chem. V. 60 2006 2017.
ISSN: ISSN 1520-4804
PubMed: 28165241
DOI: 10.1021/ACS.JMEDCHEM.6B01743
Page generated: Sun Aug 11 21:23:43 2024

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