Iodine in PDB 8c3o: Crystal Structure of Autotaxin Gamma and Compound Mey-003

All present enzymatic activity of Crystal Structure of Autotaxin Gamma and Compound Mey-003:
3.1.4.39;

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003, PDB code: 8c3o 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)	57.64 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.925, 288.478, 57.643, 90, 90.12, 90
R / Rfree (%)	21.4 / 27.1

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003 also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Autotaxin Gamma and Compound Mey-003 (pdb code 8c3o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 37 binding sites of Iodine where determined in the Crystal Structure of Autotaxin Gamma and Compound Mey-003, PDB code: 8c3o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I909 b:92.7 occ:1.00 N A:CYS86 3.6 49.9 1.0 N A:SER85 3.7 52.1 1.0 C A:THR84 3.8 50.8 1.0 CA A:THR84 3.8 49.9 1.0 CB A:CYS86 4.0 49.6 1.0 SG A:CYS86 4.0 59.7 1.0 CD A:LYS81 4.2 38.0 1.0 CG2 A:THR84 4.3 63.6 1.0 CA A:CYS86 4.3 54.5 1.0 NZ A:LYS81 4.4 37.9 1.0 O A:CYS80 4.5 48.8 1.0 CA A:SER85 4.5 50.6 1.0 O A:THR84 4.5 50.3 1.0 C A:SER85 4.5 52.1 1.0 CA A:LYS81 4.6 38.4 1.0 CB A:THR84 4.7 56.3 1.0 CE A:LYS81 4.8 37.8 1.0 O A:CYS86 4.8 64.4 1.0 N A:THR84 4.8 54.0 1.0 O A:LYS81 4.9 46.4 1.0 C A:CYS86 4.9 61.4 1.0

Iodine binding site 2 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I910 b:103.1 occ:1.00 N A:ARG626 3.8 21.8 1.0 CA A:GLY625 3.8 23.5 1.0 CD A:LYS866 3.8 36.6 1.0 CE A:LYS866 4.3 40.0 1.0 C A:GLY625 4.3 23.7 1.0 CG A:LYS866 4.3 26.8 1.0 CG A:ARG626 4.4 24.6 0.2 CG A:ARG626 4.4 24.5 0.8 NH1 A:ARG626 4.5 30.4 0.8 CB A:ARG626 4.7 24.1 0.8 CB A:ARG626 4.8 24.2 0.2 NZ A:LYS866 4.8 32.4 1.0 CD A:ARG626 4.8 26.2 0.2 CA A:ARG626 4.9 24.7 0.8 CA A:ARG626 4.9 24.7 0.2 NE A:ARG626 4.9 28.0 0.2 N A:GLY625 5.0 20.0 1.0

Iodine binding site 3 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I911 b:98.4 occ:1.00 CZ A:PHE803 3.9 17.1 1.0 CE2 A:PHE803 4.1 17.7 1.0

Iodine binding site 4 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I912 b:94.4 occ:1.00 CE1 A:HIS772 3.8 25.9 1.0 CE2 A:TYR631 3.8 20.9 1.0 CE1 A:PHE651 3.8 26.9 1.0 CA A:THR774 3.9 33.3 1.0 CZ A:PHE651 3.9 24.5 1.0 CG2 A:THR774 3.9 31.9 1.0 CD2 A:TYR631 4.0 21.5 1.0 CB A:THR774 4.2 32.2 1.0 NE2 A:HIS772 4.2 23.8 1.0 N A:GLU775 4.4 37.2 1.0 C A:THR774 4.6 35.7 1.0 O A:ASP773 4.7 22.2 1.0 CG A:GLU775 4.8 38.6 1.0 CZ A:TYR631 4.9 22.6 1.0 N A:THR774 4.9 30.3 1.0 ND1 A:HIS772 4.9 23.6 1.0

Iodine binding site 5 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I913 b:133.7 occ:1.00 O A:PRO72 3.4 95.2 1.0 C A:PRO72 4.3 89.2 1.0 CA A:PRO72 4.4 93.1 1.0 CB A:PRO72 4.8 85.1 1.0

Iodine binding site 6 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I914 b:111.0 occ:1.00 CG1 A:VAL279 3.8 40.6 1.0 CB A:SER277 4.0 35.4 1.0 N A:VAL278 4.0 25.3 1.0 CG2 A:VAL279 4.1 26.3 1.0 CB A:LYS81 4.1 36.4 1.0 N A:VAL279 4.2 28.6 1.0 CG2 A:VAL278 4.2 21.6 1.0 O A:LYS81 4.3 46.4 1.0 C A:LYS81 4.4 41.7 1.0 CB A:VAL279 4.5 31.7 1.0 C A:SER277 4.6 27.7 1.0 CA A:SER277 4.6 26.2 1.0 OG A:SER277 4.6 37.7 1.0 OG A:SER82 4.6 39.9 1.0 N A:SER82 4.6 39.0 1.0 CG1 A:VAL278 4.8 28.6 1.0 CA A:VAL278 4.8 29.3 1.0 CA A:SER82 4.8 42.2 1.0 CB A:VAL278 4.8 29.8 1.0 CA A:LYS81 4.9 38.4 1.0 C A:VAL278 4.9 30.4 1.0 CA A:VAL279 5.0 26.9 1.0

Iodine binding site 7 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I915 b:98.0 occ:1.00 N A:ARG450 3.5 17.7 1.0 CA A:GLU449 3.8 17.5 1.0 CG A:ARG450 4.0 26.5 1.0 CG2 A:VAL481 4.0 18.8 1.0 C A:GLU449 4.1 17.2 1.0 O A:VAL448 4.3 15.5 1.0 CB A:ARG450 4.3 19.2 1.0 CG A:GLU449 4.4 20.0 1.0 CA A:ARG450 4.5 21.4 1.0 CB A:GLU449 4.6 18.8 1.0 N A:GLU449 4.8 15.5 1.0 C A:VAL448 4.9 13.4 1.0

Iodine binding site 8 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I916 b:48.9 occ:1.00 N A:LEU565 3.6 35.2 1.0 O A:CYS567 3.6 59.0 1.0 CG A:PRO680 3.7 25.6 1.0 O A:PHE563 3.8 36.2 1.0 N A:CYS567 3.8 52.8 1.0 CB A:LEU565 3.9 34.8 1.0 CB A:PHE563 4.0 34.3 1.0 N A:GLY566 4.1 34.9 1.0 C A:PHE563 4.1 34.0 1.0 CA A:LEU565 4.2 28.7 1.0 CB A:CYS567 4.2 52.9 1.0 CG A:LEU565 4.3 29.1 1.0 CA A:CYS567 4.4 53.7 1.0 C A:CYS567 4.4 55.7 1.0 C A:ASP564 4.5 35.4 1.0 C A:LEU565 4.5 29.7 1.0 N A:ASP564 4.5 32.5 1.0 CA A:ASP564 4.5 34.9 1.0 CD A:PRO680 4.6 26.3 1.0 CB A:PRO680 4.7 23.3 1.0 CA A:PHE563 4.7 32.1 1.0 CD1 A:LEU565 4.8 26.4 1.0 C A:GLY566 4.8 38.7 1.0 CA A:GLY566 4.9 33.1 1.0

Iodine binding site 9 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I917 b:83.1 occ:1.00 CD A:ARG743 4.0 28.3 1.0 CA A:TYR740 4.1 17.0 1.0 NH1 A:ARG743 4.2 28.6 1.0 N A:TYR740 4.2 16.1 1.0 O A:ASN739 4.2 22.5 1.0 C A:ASN739 4.3 19.4 1.0 CB A:ASN739 4.4 20.6 1.0 CB A:ARG743 4.5 21.9 1.0 CD1 A:TYR740 4.7 18.1 1.0 CB A:TYR740 4.7 17.6 1.0 CG2 A:VAL744 4.7 16.4 1.0 OE1 A:GLU837 4.7 32.9 1.0 CG A:ARG743 4.8 22.5 1.0 NE A:ARG743 5.0 34.2 1.0

Iodine binding site 10 out of 37 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


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 and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:I918 b:111.3 occ:1.00 N A:PRO715 3.6 36.2 1.0 O A:SER712 3.6 28.5 1.0 C A:SER714 3.7 32.2 1.0 OG A:SER668 3.7 44.0 1.0 CD A:PRO715 3.7 35.0 1.0 CB A:SER668 3.8 48.6 1.0 CA A:SER714 3.8 28.1 1.0 N A:SER714 4.0 25.1 1.0 CG A:PRO715 4.1 34.3 1.0 OG A:SER712 4.1 26.7 1.0 O A:SER714 4.2 37.9 1.0 CA A:PRO715 4.3 37.2 1.0 C A:SER712 4.4 26.7 1.0 CE A:LYS718 4.4 35.0 1.0 C A:SER713 4.5 25.6 1.0 NZ A:LYS718 4.5 33.0 1.0 CB A:SER712 4.6 28.3 1.0 O A:SER713 4.8 31.1 1.0 CB A:PRO715 4.8 34.9 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