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Iodine in PDB 5m0m: 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: 5m0m 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) 75.27 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.995, 89.173, 77.289, 90.00, 103.12, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 5m0m:

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) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 5m0m

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Iodine binding site 1 out of 12 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:I910

b:32.6
occ:1.00
 N A:ASN230 3.5 24.1 1.0
NH1 A:ARG391 3.6 26.7 1.0
CA A:GLY229 3.9 22.6 1.0
N A:SER231 4.0 26.4 1.0
CE A:LYS208 4.1 26.2 1.0
C A:GLY229 4.1 23.2 1.0
O A:SER231 4.2 25.4 1.0
CG A:LYS208 4.2 24.6 1.0
CG1 A:VAL385 4.3 28.9 1.0
CD1 A:LEU389 4.4 29.2 1.0
CA A:ASN230 4.4 25.4 1.0
CB A:ASN230 4.5 25.8 1.0
CD A:LYS208 4.6 25.4 1.0
C A:ASN230 4.7 25.9 1.0
CZ A:ARG391 4.8 26.8 1.0
CD2 A:LEU389 4.8 28.0 1.0
CA A:SER231 4.9 27.1 1.0
CB A:SER231 4.9 28.2 1.0
CG A:LEU389 4.9 28.5 1.0
C A:SER231 5.0 26.6 1.0

Iodine binding site 2 out of 12 in 5m0m

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Iodine binding site 2 out of 12 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:I911

b:71.0
occ:0.76
 OD1 A:ASP782 3.6 58.2 1.0
N A:ASP782 3.7 52.3 1.0
CG A:ASP782 3.8 57.2 1.0
N A:ALA781 3.8 51.3 1.0
CA A:SER636 3.9 48.2 1.0
CB A:ALA781 4.1 49.2 1.0
CB A:ASP782 4.1 55.0 1.0
CA A:GLY729 4.2 39.4 1.0
CB A:SER636 4.2 49.4 1.0
CG2 A:THR634 4.2 38.6 1.0
CB A:PRO780 4.3 55.3 1.0
OD2 A:ASP782 4.3 58.3 1.0
CA A:ALA781 4.3 50.0 1.0
N A:SER636 4.4 46.3 1.0
C A:ALA781 4.5 50.3 1.0
O A:ASN728 4.5 41.2 1.0
CA A:ASP782 4.5 53.3 1.0
O A:ILE635 4.5 43.9 1.0
C A:PRO780 4.6 52.3 1.0
C A:ILE635 4.7 44.1 1.0
C A:GLY729 4.8 37.5 1.0
CA A:PRO780 4.9 54.4 1.0
C A:SER636 5.0 50.1 1.0

Iodine binding site 3 out of 12 in 5m0m

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Iodine binding site 3 out of 12 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:I912

b:66.3
occ:0.73
 OE1 A:GLU847 2.8 39.9 1.0
N A:LEU788 3.6 41.8 1.0
CD A:GLU847 3.7 38.9 1.0
CG A:GLU847 3.8 36.3 1.0
O A:GLU847 4.1 30.1 1.0
CB A:LEU788 4.1 39.8 1.0
NH1 A:ARG843 4.2 49.1 1.0
CA A:PRO787 4.2 45.8 1.0
CB A:LEU851 4.2 25.9 1.0
CG A:ARG843 4.2 42.6 1.0
CD1 A:LEU851 4.3 26.8 1.0
CA A:LEU788 4.4 40.4 1.0
O A:LEU788 4.4 38.9 1.0
CG A:LEU788 4.4 40.3 1.0
CD2 A:LEU851 4.4 27.2 1.0
C A:PRO787 4.4 44.3 1.0
CB A:PRO787 4.4 45.0 1.0
CD1 A:ILE848 4.5 31.5 1.0
CG A:LEU851 4.5 26.4 1.0
C A:GLU847 4.6 30.9 1.0
CB A:GLU847 4.7 35.0 1.0
CB A:ARG843 4.7 41.1 1.0
C A:LEU788 4.8 38.9 1.0
OE2 A:GLU847 4.8 40.9 1.0
CD1 A:LEU788 4.9 39.6 1.0

Iodine binding site 4 out of 12 in 5m0m

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Iodine binding site 4 out of 12 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:I913

b:62.6
occ:0.65
 OG1 A:THR334 3.2 25.9 1.0
ND1 A:HIS281 3.3 38.5 1.0
OG A:SER307 3.4 30.4 1.0
CE1 A:HIS281 3.6 38.6 1.0
CG A:HIS281 3.7 37.4 1.0
CD1 A:ILE331 3.7 31.0 1.0
CB A:THR334 3.8 26.0 1.0
CB A:SER307 3.9 30.2 1.0
CA A:ILE331 4.1 30.5 1.0
CG2 A:THR334 4.1 25.6 1.0
NE2 A:HIS281 4.3 37.9 1.0
CB A:HIS281 4.3 36.2 1.0
CD2 A:HIS281 4.3 37.7 1.0
O A:GLU330 4.3 32.5 1.0
N A:ILE331 4.4 31.7 1.0
CZ A:PHE305 4.4 31.4 1.0
CE2 A:PHE305 4.5 30.9 1.0
C A:GLU330 4.5 33.2 1.0
CB A:ILE331 4.8 30.0 1.0
CG2 A:ILE331 4.8 29.5 1.0
CG1 A:ILE331 4.9 30.7 1.0
CA A:SER307 4.9 30.1 1.0
O A:ILE331 5.0 28.8 1.0

Iodine binding site 5 out of 12 in 5m0m

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Iodine binding site 5 out of 12 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:I914

b:90.9
occ:0.59
 N A:ASN399 3.9 63.2 1.0
CB A:ASN399 4.0 64.9 1.0
CA A:ASN399 4.1 65.0 1.0
C A:ASN398 4.1 62.5 1.0
CB A:ASN398 4.1 62.5 1.0
O A:ASN398 4.4 64.6 1.0
CG A:ASN399 4.6 66.3 1.0
OD1 A:ASN399 4.6 68.2 1.0
CB A:SER396 4.7 52.1 1.0
CA A:ASN398 4.7 61.3 1.0
OG A:SER396 4.8 53.2 1.0

Iodine binding site 6 out of 12 in 5m0m

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Iodine binding site 6 out of 12 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:I915

b:60.4
occ:0.88
 CD A:PRO457 3.9 49.5 1.0
CG A:LEU458 3.9 55.2 1.0
N A:LEU458 4.0 52.8 1.0
CB A:LEU458 4.2 54.4 1.0
N A:PRO457 4.3 48.5 1.0
CE A:LYS456 4.3 53.4 1.0
CB A:PRO457 4.4 50.9 1.0
CD1 A:LEU458 4.4 57.2 1.0
CB A:LYS456 4.5 48.3 1.0
CG A:PRO457 4.5 50.5 1.0
CA A:PRO457 4.7 49.8 1.0
CG A:LYS456 4.7 50.0 1.0
CA A:LEU458 4.7 53.5 1.0
C A:PRO457 4.8 51.1 1.0
C A:LYS456 5.0 46.5 1.0

Iodine binding site 7 out of 12 in 5m0m

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Iodine binding site 7 out of 12 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:I916

b:50.5
occ:0.70
 NH2 A:ARG393 3.5 37.5 1.0
C A:MET232 3.7 27.8 1.0
O A:MET232 3.8 28.6 1.0
N A:TYR233 3.9 28.1 1.0
N A:MET232 3.9 26.7 1.0
CA A:MET232 4.1 26.9 1.0
CG2 A:VAL385 4.2 29.2 1.0
CE1 A:HIS242 4.2 32.5 1.0
CB A:TYR233 4.2 29.5 1.0
CB A:SER231 4.3 28.2 1.0
C A:SER231 4.4 26.6 1.0
OG A:SER240 4.4 32.3 1.0
CA A:TYR233 4.5 29.0 1.0
CZ A:ARG393 4.6 38.2 1.0
NE2 A:HIS242 4.7 33.5 1.0
O A:SER231 4.8 25.4 1.0
O A:HOH1002 4.8 25.8 1.0
NH1 A:ARG393 4.8 39.9 1.0
CA A:SER231 4.9 27.1 1.0
CB A:SER240 5.0 31.1 1.0

Iodine binding site 8 out of 12 in 5m0m

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Iodine binding site 8 out of 12 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:I917

b:63.8
occ:0.71
 O A:CYS566 3.8 56.8 1.0
N A:CYS566 3.8 54.3 1.0
N A:LEU564 3.8 52.9 1.0
O A:PHE562 3.9 55.1 1.0
CB A:LEU564 3.9 50.9 1.0
CB A:CYS566 4.0 55.6 1.0
CB A:PHE562 4.1 53.7 1.0
N A:GLY565 4.2 52.2 1.0
CA A:LEU564 4.3 51.7 1.0
CA A:CYS566 4.3 55.2 1.0
C A:CYS566 4.3 55.8 1.0
C A:PHE562 4.4 55.0 1.0
CG A:LEU564 4.4 50.8 1.0
C A:LEU564 4.5 51.5 1.0
CG A:PRO654 4.6 44.1 1.0
CD A:PRO654 4.6 43.8 1.0
SG A:CYS566 4.7 56.9 1.0
CB A:PRO654 4.7 43.1 1.0
CD1 A:LEU564 4.9 49.8 1.0
C A:GLY565 4.9 53.3 1.0
CA A:PHE562 4.9 54.6 1.0
C A:ASP563 4.9 54.0 1.0
N A:ASP563 5.0 55.4 1.0

Iodine binding site 9 out of 12 in 5m0m

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Iodine binding site 9 out of 12 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:I918

b:65.9
occ:0.56
 OG A:SER846 3.1 34.8 1.0
N A:SER846 3.9 32.6 1.0
CB A:SER846 4.0 33.2 1.0
CD A:PRO541 4.3 40.3 1.0
N A:TYR845 4.3 33.4 1.0
CA A:SER846 4.5 32.4 1.0
CB A:SER844 4.6 35.7 1.0
CB A:TYR845 4.6 33.0 1.0
CG A:PRO541 4.6 39.3 1.0
C A:TYR845 4.8 32.1 1.0
CA A:TYR845 4.8 32.8 1.0
OG A:SER844 4.9 35.1 1.0

Iodine binding site 10 out of 12 in 5m0m

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Iodine binding site 10 out of 12 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 10 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I919

b:81.4
occ:0.65
 NH1 A:ARG746 3.8 30.4 1.0
N A:GLU749 3.9 39.4 1.0
CA A:THR748 4.0 34.4 1.0
CG A:GLU749 4.2 43.4 1.0
CE1 A:PHE625 4.2 35.6 1.0
CB A:THR748 4.3 34.7 1.0
C A:THR748 4.4 36.4 1.0
CZ A:PHE625 4.4 35.1 1.0
CE2 A:TYR605 4.5 31.7 1.0
OE1 A:GLU749 4.6 45.1 1.0
CG2 A:THR748 4.7 34.4 1.0
CD2 A:TYR605 4.7 32.0 1.0
O A:ASP747 4.8 29.7 1.0
CB A:GLU749 4.9 42.7 1.0
CA A:GLU749 4.9 41.6 1.0
CD A:GLU749 4.9 44.7 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 21:24:45 2024

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