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Iodine in PDB 8c4w: Crystal Structure of Rat Autotaxin and Compound Mey-002

Enzymatic activity of Crystal Structure of Rat Autotaxin and Compound Mey-002

All present enzymatic activity of Crystal Structure of Rat Autotaxin and Compound Mey-002:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-002, PDB code: 8c4w 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) 47.65 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.228, 62.863, 70.151, 98.99, 106.57, 99.51
R / Rfree (%) 19.6 / 23.6

Other elements in 8c4w:

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-002 also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Rat Autotaxin and Compound Mey-002 (pdb code 8c4w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Rat Autotaxin and Compound Mey-002, PDB code: 8c4w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 8c4w

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Iodine binding site 1 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I903

b:29.3
occ:1.00
 N A:ASN230 3.4 27.9 1.0
NH1 A:ARG391 3.7 25.1 1.0
CA A:GLY229 3.8 18.6 1.0
NZ A:LYS208 3.9 29.3 1.0
N A:SER231 4.0 28.2 1.0
C A:GLY229 4.1 28.7 1.0
O A:SER231 4.2 26.4 1.0
CG A:LYS208 4.3 24.9 1.0
CB A:ASN230 4.3 23.5 1.0
CA A:ASN230 4.3 26.1 1.0
CG1 A:VAL385 4.4 26.9 1.0
CD2 A:LEU389 4.4 23.8 1.0
CE A:LYS208 4.4 26.4 1.0
CD1 A:LEU389 4.4 29.9 1.0
C A:ASN230 4.7 26.7 1.0
CG A:LEU389 4.7 25.8 1.0
CD A:LYS208 4.7 24.4 1.0
CZ A:ARG391 4.8 25.1 1.0
CA A:SER231 4.9 28.2 1.0
CB A:SER231 5.0 31.3 1.0

Iodine binding site 2 out of 9 in 8c4w

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Iodine binding site 2 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I904

b:53.6
occ:1.00
 NH2 A:ARG393 3.5 36.1 1.0
NH1 A:ARG393 3.6 32.0 1.0
C A:MET232 3.7 29.1 1.0
N A:TYR233 4.0 29.0 1.0
O A:MET232 4.0 28.6 1.0
N A:MET232 4.0 26.9 1.0
CZ A:ARG393 4.0 32.9 1.0
CA A:MET232 4.1 28.8 1.0
CG2 A:VAL385 4.2 30.6 1.0
CE1 A:HIS242 4.2 35.0 1.0
CB A:TYR233 4.3 29.1 1.0
CB A:SER231 4.3 31.3 1.0
C A:SER231 4.4 27.2 1.0
OG A:SER240 4.4 38.7 1.0
CB A:SER240 4.5 33.7 1.0
CA A:TYR233 4.6 28.6 1.0
O A:SER231 4.8 26.4 1.0
NE2 A:HIS242 4.8 38.6 1.0
O A:HOH1093 4.9 28.0 1.0
CA A:SER231 4.9 28.2 1.0

Iodine binding site 3 out of 9 in 8c4w

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Iodine binding site 3 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I906

b:61.7
occ:1.00
 NE2 A:HIS251 3.8 28.4 1.0
CB A:ARG252 3.8 28.9 1.0
CB A:ASN250 3.8 31.3 1.0
N A:ARG252 3.8 25.8 1.0
CG A:ARG252 3.9 29.3 1.0
CD2 A:HIS251 4.0 29.7 1.0
CD A:ARG252 4.0 31.9 1.0
CE1 A:HIS251 4.0 30.8 1.0
N A:HIS251 4.1 25.9 1.0
CG A:ASN250 4.3 35.6 1.0
CG A:HIS251 4.3 28.9 1.0
CA A:ASN250 4.3 29.6 1.0
ND1 A:HIS251 4.3 26.4 1.0
C A:ASN250 4.4 28.7 1.0
CA A:ARG252 4.4 24.3 1.0
OD1 A:ASN250 4.5 34.4 1.0
NE A:ARG252 4.8 28.4 1.0
C A:HIS251 4.8 25.9 1.0
CA A:HIS251 4.9 29.4 1.0
ND2 A:ASN250 5.0 37.3 1.0

Iodine binding site 4 out of 9 in 8c4w

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Iodine binding site 4 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I915

b:198.2
occ:1.00
 OG1 A:THR52 3.0 156.2 1.0
CG2 A:THR52 3.4 120.3 1.0
CB A:THR52 3.7 143.1 1.0
CA A:THR52 4.4 150.6 1.0
CB A:PRO70 5.0 182.0 1.0

Iodine binding site 5 out of 9 in 8c4w

Go back to Iodine Binding Sites List in 8c4w
Iodine binding site 5 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I916

b:79.0
occ:1.00
 CG A:PRO654 3.8 53.9 1.0
CB A:LEU564 3.8 57.8 1.0
N A:LEU564 3.9 68.5 1.0
O A:CYS566 3.9 58.4 1.0
O A:PHE562 4.0 68.1 1.0
CB A:PHE562 4.0 65.6 1.0
CG A:LEU564 4.1 58.2 1.0
N A:CYS566 4.2 56.3 1.0
CB A:CYS566 4.3 57.0 1.0
CA A:LEU564 4.3 61.5 1.0
C A:PHE562 4.4 71.6 1.0
CD A:PRO654 4.4 48.8 1.0
N A:GLY565 4.5 57.1 1.0
CB A:PRO654 4.6 49.2 1.0
CA A:CYS566 4.6 58.2 1.0
CD1 A:LEU564 4.6 51.3 1.0
C A:CYS566 4.6 57.9 1.0
C A:LEU564 4.8 59.9 1.0
CA A:PHE562 4.9 69.8 1.0
N A:ASP563 4.9 73.4 1.0
C A:ASP563 4.9 70.1 1.0

Iodine binding site 6 out of 9 in 8c4w

Go back to Iodine Binding Sites List in 8c4w
Iodine binding site 6 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I917

b:87.9
occ:1.00
 O A:VAL453 3.8 28.8 1.0
CA A:GLY387 3.9 28.5 1.0
N A:GLY387 4.0 26.5 1.0
ND1 A:HIS452 4.0 34.1 1.0
CB A:ALA454 4.1 33.5 1.0
CG A:HIS452 4.1 31.8 1.0
CB A:PRO386 4.2 27.2 1.0
CB A:HIS452 4.2 29.1 1.0
C A:VAL453 4.5 30.9 1.0
C A:PRO386 4.6 29.5 1.0
CA A:ALA454 4.6 32.2 1.0
CG A:PRO386 4.6 28.1 1.0
CE1 A:HIS452 4.7 30.5 1.0
N A:ALA454 4.8 28.9 1.0
CD2 A:HIS452 4.8 29.7 1.0

Iodine binding site 7 out of 9 in 8c4w

Go back to Iodine Binding Sites List in 8c4w
Iodine binding site 7 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I918

b:65.7
occ:1.00
 NH2 A:ARG746 3.5 38.9 1.0
N A:GLU749 3.7 40.3 1.0
O A:HOH1063 4.0 46.4 1.0
CA A:THR748 4.1 34.7 1.0
C A:THR748 4.4 38.6 1.0
CB A:GLU749 4.5 44.2 1.0
CB A:THR748 4.5 36.3 1.0
CZ A:PHE625 4.5 49.6 1.0
CA A:GLU749 4.7 41.9 1.0
CE2 A:TYR605 4.7 34.6 1.0
CG2 A:THR748 4.7 34.0 1.0
CZ A:ARG746 4.8 40.1 1.0
CD2 A:TYR605 4.8 35.6 1.0
O A:ARG606 4.9 33.7 1.0
CE1 A:PHE625 4.9 47.9 1.0

Iodine binding site 8 out of 9 in 8c4w

Go back to Iodine Binding Sites List in 8c4w
Iodine binding site 8 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I919

b:52.3
occ:1.00
 O A:HOH1208 3.2 29.2 1.0
N A:ASP782 3.6 33.1 1.0
OD1 A:ASP782 3.6 35.0 1.0
CG A:ASP782 3.8 37.4 1.0
CA A:SER636 3.8 28.8 1.0
N A:ALA781 3.9 29.7 1.0
CB A:ASP782 3.9 37.8 1.0
CB A:SER636 4.0 30.9 1.0
CG2 A:THR634 4.1 28.2 1.0
CA A:GLY729 4.1 22.5 1.0
CB A:PRO780 4.2 33.4 1.0
CB A:ALA781 4.3 24.9 1.0
O A:ASN728 4.4 26.5 1.0
O A:HOH1249 4.4 55.7 1.0
CA A:ASP782 4.4 34.9 1.0
CA A:ALA781 4.4 27.7 1.0
OD2 A:ASP782 4.4 44.4 1.0
C A:ALA781 4.4 33.6 1.0
N A:SER636 4.4 31.3 1.0
C A:PRO780 4.6 28.7 1.0
O A:ILE635 4.7 29.6 1.0
CA A:PRO780 4.7 32.2 1.0
C A:ILE635 4.8 28.6 1.0
C A:GLY729 4.9 24.7 1.0
N A:LYS637 4.9 26.9 1.0
C A:SER636 4.9 27.3 1.0
N A:GLY729 5.0 20.8 1.0

Iodine binding site 9 out of 9 in 8c4w

Go back to Iodine Binding Sites List in 8c4w
Iodine binding site 9 out of 9 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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 Rat Autotaxin and Compound Mey-002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I920

b:75.2
occ:1.00
 OE1 A:GLN716 2.8 35.8 1.0
O A:HOH1290 3.3 34.5 1.0
N A:PHE679 3.8 27.4 1.0
O A:PHE679 3.9 26.3 1.0
CD A:GLN716 4.0 34.3 1.0
CD1 A:TRP712 4.0 25.7 1.0
CE2 A:TYR684 4.1 42.8 1.0
NE1 A:TRP712 4.3 28.1 1.0
CD A:PRO683 4.4 35.5 1.0
CB A:PHE679 4.4 29.4 1.0
CA A:PHE679 4.5 29.8 1.0
S A:SCN911 4.5 77.8 1.0
CA A:GLY678 4.6 27.9 1.0
C A:PHE679 4.7 29.7 1.0
CD2 A:PHE679 4.7 34.0 1.0
NE2 A:GLN716 4.7 31.1 1.0
C A:GLY678 4.7 30.7 1.0
OH A:TYR684 4.7 43.9 1.0
CB A:GLN716 4.9 26.6 1.0
CZ A:TYR684 4.9 42.2 1.0
CD2 A:TYR684 4.9 38.3 1.0
CA A:ALA713 5.0 24.8 1.0

Reference:

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
Page generated: Mon Aug 12 02:31:37 2024

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