Iodine in PDB 8c3p: Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1

All present enzymatic activity of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1:
3.1.4.39;

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p was solved by M.C.Eymery, A.A.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.88 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.94, 57.22, 287.926, 90, 92.72, 90
R / Rfree (%)	22.2 / 28

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 (pdb code 8c3p). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I903 b:80.3 occ:1.00 N A:LEU565 3.5 61.1 1.0 CG A:PRO680 3.6 44.4 1.0 O A:PHE563 3.9 53.7 1.0 CB A:PHE563 4.0 52.4 1.0 C A:PHE563 4.1 51.6 1.0 O A:CYS567 4.1 53.1 1.0 CB A:LEU565 4.1 59.9 1.0 CG A:LEU565 4.2 53.1 1.0 N A:CYS567 4.2 58.4 1.0 CA A:LEU565 4.3 63.0 1.0 CA A:ASP564 4.3 57.1 1.0 N A:ASP564 4.3 57.8 1.0 N A:GLY566 4.3 53.2 1.0 C A:ASP564 4.4 62.8 1.0 CD A:PRO680 4.5 52.4 1.0 CB A:CYS567 4.6 65.0 1.0 C A:LEU565 4.6 55.0 1.0 CD1 A:LEU565 4.6 51.2 1.0 CB A:PRO680 4.7 48.5 1.0 CA A:PHE563 4.7 56.4 1.0 CA A:CYS567 4.8 67.4 1.0 C A:CYS567 4.9 62.0 1.0

Iodine binding site 2 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:71.1 occ:1.00 OD1 A:ASP808 3.4 53.0 1.0 CG A:ASP808 3.6 43.7 1.0 O A:HOH1011 3.7 40.6 1.0 N A:ALA807 3.7 39.1 1.0 N A:ASP808 3.7 40.6 1.0 CA A:SER662 3.9 41.3 1.0 CG2 A:THR660 3.9 31.8 1.0 CB A:ALA807 4.0 33.7 1.0 OD2 A:ASP808 4.0 45.3 1.0 CB A:SER662 4.1 42.6 1.0 CA A:GLY755 4.1 42.5 1.0 CB A:PRO806 4.2 32.6 1.0 CB A:ASP808 4.2 43.8 1.0 CA A:ALA807 4.3 34.7 1.0 O A:VAL661 4.4 41.4 1.0 O A:ASN754 4.4 38.9 1.0 C A:ALA807 4.5 39.6 1.0 N A:SER662 4.5 30.9 1.0 C A:PRO806 4.6 43.7 1.0 CA A:ASP808 4.6 42.6 1.0 C A:VAL661 4.7 30.9 1.0 CA A:PRO806 4.7 36.4 1.0 C A:GLY755 4.8 42.0 1.0 C A:SER662 5.0 42.5 1.0

Iodine binding site 3 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:69.8 occ:1.00 O A:HOH1066 3.3 39.5 1.0 O A:HOH1150 3.3 34.8 1.0 O A:HOH1192 3.6 40.6 1.0 N A:LEU814 3.8 38.1 1.0 O A:GLU873 4.0 27.6 1.0 CA A:PRO813 4.0 33.2 1.0 CB A:PRO813 4.1 32.4 1.0 CG A:ARG869 4.2 44.7 1.0 CB A:LEU877 4.2 28.2 1.0 CD1 A:ILE874 4.2 38.2 1.0 CD1 A:LEU877 4.2 36.2 1.0 CD2 A:LEU877 4.3 36.7 1.0 C A:PRO813 4.4 39.5 1.0 NE A:ARG869 4.4 44.3 1.0 CG A:LEU877 4.5 37.5 1.0 C A:GLU873 4.5 33.0 1.0 CB A:ARG869 4.5 40.6 1.0 CB A:GLU873 4.6 35.1 1.0 O A:LEU814 4.7 35.8 1.0 CG A:LEU814 4.7 42.0 1.0 CB A:LEU814 4.7 43.6 1.0 CA A:LEU814 4.7 36.9 1.0 CD A:ARG869 4.8 50.7 1.0 N A:ILE874 5.0 34.8 1.0

Iodine binding site 4 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I910 b:115.4 occ:1.00 CG2 A:THR774 3.6 49.1 1.0 CE2 A:TYR631 3.9 37.4 1.0 CA A:THR774 3.9 44.6 1.0 CB A:THR774 4.1 42.7 1.0 CD2 A:TYR631 4.1 35.8 1.0 N A:GLU775 4.1 49.9 1.0 CG A:GLU775 4.2 62.9 1.0 NE2 A:HIS772 4.2 44.6 1.0 CE1 A:PHE651 4.3 49.3 1.0 CZ A:PHE651 4.4 35.3 1.0 O A:ARG632 4.5 42.1 1.0 C A:THR774 4.6 46.5 1.0 OE2 A:GLU775 4.7 69.4 1.0 O A:ASP773 4.7 42.3 1.0 O A:HOH1216 4.7 43.9 1.0 CD A:GLU775 4.9 66.3 1.0 CE1 A:HIS772 5.0 38.4 1.0

Iodine binding site 5 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I911 b:153.0 occ:1.00 O5 C:NAG2 3.3 53.1 1.0 O A:HOH1024 3.4 28.8 1.0 O3 C:NAG1 3.4 40.4 1.0 O6 C:NAG2 3.5 64.0 1.0 O4 C:NAG1 3.7 45.3 1.0 ND2 A:ASN437 3.8 32.7 1.0 C1 C:NAG2 4.0 42.6 1.0 C3 C:NAG1 4.1 33.1 1.0 C5 C:NAG2 4.4 53.9 1.0 C6 C:NAG2 4.4 54.2 1.0 CD1 A:LEU771 4.4 30.9 1.0 C2 C:NAG2 4.4 53.5 1.0 C4 C:NAG1 4.5 38.2 1.0 CB A:ASP769 4.5 29.8 1.0 OD2 A:ASP769 4.5 32.8 1.0 O7 C:NAG2 4.8 60.0 1.0 C4 C:NAG2 4.8 55.0 1.0 O A:ASP769 4.9 31.2 1.0 CG A:ASP769 5.0 37.5 1.0

Iodine binding site 6 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I912 b:64.7 occ:0.47 O A:HOH1184 3.5 36.6 1.0 ND1 A:HIS453 3.5 42.5 1.0 N A:GLY388 3.7 37.5 1.0 O A:VAL454 3.7 36.8 1.0 CA A:GLY388 3.9 37.5 1.0 CB A:PRO387 4.0 26.9 1.0 CB A:ALA455 4.1 37.3 1.0 CG A:HIS453 4.1 36.3 1.0 CE1 A:HIS453 4.2 45.2 1.0 CB A:HIS453 4.4 27.6 1.0 C A:PRO387 4.5 37.9 1.0 C A:VAL454 4.5 31.6 1.0 CG2 A:THR370 4.6 44.9 1.0 CG A:PRO387 4.6 36.6 1.0 CA A:ALA455 4.8 32.8 1.0 CA A:PRO387 4.8 34.7 1.0 N A:ALA455 5.0 32.5 1.0 N A:VAL454 5.0 27.9 1.0 C A:GLY388 5.0 31.3 1.0 CD2 A:HIS453 5.0 45.2 1.0

Iodine binding site 7 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I913 b:107.9 occ:1.00 NH2 A:ARG394 3.5 39.2 1.0 C A:MET233 3.7 34.9 1.0 N A:MET233 3.7 29.4 1.0 O A:MET233 3.9 36.7 1.0 CG2 A:THR241 3.9 42.2 1.0 CA A:MET233 3.9 33.8 1.0 CB A:SER232 4.0 34.5 1.0 N A:TYR234 4.1 36.6 1.0 CG2 A:VAL386 4.1 42.1 1.0 C A:SER232 4.1 34.1 1.0 CZ A:ARG394 4.4 46.5 1.0 NH1 A:ARG394 4.4 39.0 1.0 CB A:TYR234 4.5 39.6 1.0 CA A:SER232 4.6 38.5 1.0 O A:SER232 4.7 39.1 1.0 CA A:TYR234 4.7 36.6 1.0 CE1 A:HIS243 4.9 49.4 1.0 O A:PHE242 5.0 45.6 1.0

Iodine binding site 8 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I914 b:39.0 occ:1.00 O A:HOH1174 3.3 43.6 1.0 N A:ASN231 3.6 29.7 1.0 CD A:LYS209 3.7 30.2 0.5 CE A:LYS209 3.8 33.4 0.5 CD2 A:LEU390 3.8 41.1 1.0 NH1 A:ARG392 3.9 42.5 1.0 CA A:GLY230 3.9 21.6 1.0 N A:SER232 4.1 35.0 1.0 NZ A:LYS209 4.2 28.3 0.5 C A:GLY230 4.2 30.6 1.0 O A:SER232 4.2 39.1 1.0 CB A:ASN231 4.4 29.3 1.0 CG1 A:VAL386 4.4 35.2 1.0 CA A:ASN231 4.4 33.4 1.0 CG A:LYS209 4.5 31.9 0.5 CG A:LYS209 4.5 32.1 0.5 CE A:LYS209 4.6 32.0 0.5 CD1 A:LEU390 4.7 29.8 1.0 CG A:LEU390 4.7 34.8 1.0 C A:ASN231 4.8 31.6 1.0 CZ A:ARG392 4.9 40.8 1.0 CA A:SER232 5.0 38.5 1.0

Iodine binding site 9 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ A:I915 b:119.7 occ:1.00 NZ A:LYS81 3.5 72.1 1.0 SG A:CYS86 3.7 77.8 1.0 CA A:THR84 3.7 70.6 1.0 N A:CYS86 3.7 63.7 1.0 CG2 A:THR84 3.7 71.3 1.0 C A:THR84 3.8 64.6 1.0 N A:SER85 3.9 72.7 1.0 CB A:CYS86 4.0 68.8 1.0 CB A:THR84 4.4 66.9 1.0 CA A:CYS86 4.4 67.7 1.0 CE A:LYS81 4.4 76.5 1.0 O A:THR84 4.4 62.4 1.0 O A:CYS80 4.5 63.6 1.0 CD A:LYS81 4.6 68.0 1.0 O A:CYS86 4.6 65.7 1.0 C A:SER85 4.7 71.1 1.0 CA A:SER85 4.7 70.2 1.0 N A:THR84 4.8 69.9 1.0 CA A:LYS81 4.8 58.8 1.0 C A:CYS86 4.9 71.5 1.0 O A:LYS81 5.0 68.9 1.0

Iodine binding site 10 out of 17 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range: probe atom residue distance (Å) B Occ B:I904 b:62.1 occ:1.00 CD B:ARG869 3.4 38.8 1.0 N B:LEU814 3.7 37.1 1.0 CG B:ARG869 3.7 37.6 1.0 O B:HOH1028 3.7 40.4 1.0 O B:GLU873 4.1 36.1 1.0 CA B:PRO813 4.2 35.0 1.0 CD1 B:LEU877 4.2 23.0 1.0 CB B:LEU877 4.3 33.9 1.0 CB B:ARG869 4.4 38.5 1.0 CD2 B:LEU877 4.4 28.6 1.0 CB B:LEU814 4.4 27.6 1.0 CB B:PRO813 4.4 34.8 1.0 CB B:GLU873 4.5 34.1 1.0 C B:GLU873 4.5 34.8 1.0 C B:PRO813 4.5 39.1 1.0 CG B:LEU877 4.5 31.9 1.0 CD1 B:ILE874 4.6 36.5 1.0 CA B:LEU814 4.6 36.5 1.0 O B:LEU814 4.6 36.4 1.0 NE B:ARG869 4.8 41.4 1.0 CG B:LEU814 4.8 35.7 1.0 NH1 B:ARG869 5.0 43.0 1.0 N B:ILE874 5.0 37.1 1.0

M.C.Eymery, K.A.Nguyen, S.Basu, J.Hausmann, V.K.T.Nguyen, H.P.Seidel, L.Gutierrez, A.Boumendjel, A.A.Mccarthy. Discovery of Potent Chromone-Based Autotaxin Inhibitors Inspired By Cannabinoids Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115944