Iodine in PDB 7lml: Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid

The structure of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid, PDB code: 7lml was solved by L.E.Salay, N.Kozlyuk, B.A.Gilston, R.D.Gogliotti, P.P.Christov, K.Kim, M.Ovee, A.G.Waterson, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.70 / 2.15
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	102.478, 102.478, 102.158, 90, 90, 120
R / Rfree (%)	21.2 / 23.5

The structure of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iodine atom in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid (pdb code 7lml). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid, PDB code: 7lml:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:140.8 occ:0.71 I13 A:Y6S305 0.0 140.8 0.7 C01 A:Y6S305 2.1 52.3 0.7 C02 A:Y6S305 3.1 57.0 0.7 C06 A:Y6S305 3.2 17.5 0.7 CG A:GLN100 3.5 46.0 1.0 CD A:GLN100 3.8 58.7 1.0 NE2 A:GLN100 3.9 65.5 1.0 CG A:GLU108 4.0 59.7 1.0 C A:ALA101 4.3 36.3 1.0 CB A:MET102 4.3 48.3 1.0 N A:MET102 4.4 41.8 1.0 O A:ALA101 4.4 31.9 1.0 OE1 A:GLN100 4.4 50.8 1.0 C05 A:Y6S305 4.6 29.6 0.7 C03 A:Y6S305 4.6 62.6 0.7 N A:ALA101 4.6 28.5 1.0 C A:GLN100 4.7 27.3 1.0 CB A:GLU108 4.7 44.5 1.0 CA A:ALA101 4.8 34.0 1.0 O A:GLN100 4.8 26.2 1.0 CA A:MET102 4.8 57.5 1.0 CB A:GLN100 4.8 33.5 1.0 CD A:GLU108 4.9 73.0 1.0 O A:ARG48 5.0 31.8 1.0

Iodine binding site 2 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:61.6 occ:1.00 I13 A:Y6S306 0.0 61.6 1.0 C01 A:Y6S306 2.1 40.7 1.0 C06 A:Y6S306 3.1 31.8 1.0 C02 A:Y6S306 3.1 37.7 1.0 CD2 A:LEU79 3.8 19.2 1.0 I13 A:Y6S307 3.9 103.3 0.6 CD2 A:PHE85 3.9 22.6 1.0 C02 B:Y6S307 4.1 48.4 0.6 CE2 B:PHE85 4.1 25.1 1.0 CB A:ARG77 4.4 29.8 1.0 CE2 A:PHE85 4.4 27.6 1.0 CD A:ARG77 4.5 46.9 1.0 C05 A:Y6S306 4.5 40.2 1.0 C01 B:Y6S307 4.6 52.0 0.6 C03 A:Y6S306 4.6 51.5 1.0 CB B:PRO87 4.7 20.5 1.0 CZ B:PHE85 4.7 19.2 1.0 C03 B:Y6S307 4.8 54.2 0.6 CG A:PHE85 4.8 16.7 1.0 I13 B:Y6S307 4.9 104.0 0.6

Iodine binding site 3 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:103.3 occ:0.59 I13 A:Y6S307 0.0 103.3 0.6 C01 A:Y6S307 2.1 48.7 0.6 C06 A:Y6S307 3.1 54.9 0.6 C02 A:Y6S307 3.2 36.7 0.6 NE A:ARG77 3.7 44.8 1.0 O A:ASP73 3.9 31.2 1.0 I13 A:Y6S306 3.9 61.6 1.0 CD A:ARG77 3.9 46.9 1.0 CD A:PRO87 4.0 23.4 1.0 CD2 A:PHE85 4.0 22.6 1.0 CB A:ARG77 4.1 29.8 1.0 CG A:ARG77 4.1 37.0 1.0 CG A:PRO87 4.2 31.4 1.0 CE2 A:PHE85 4.3 27.6 1.0 CZ A:ARG77 4.3 57.5 1.0 C05 A:Y6S307 4.5 49.1 0.6 N A:ARG77 4.6 18.4 1.0 C03 A:Y6S307 4.6 47.9 0.6 O A:PHE85 4.6 12.8 1.0 C06 B:Y6S305 4.7 32.6 0.7 NH2 A:ARG77 4.7 41.1 1.0 I13 B:Y6S305 4.9 43.2 0.7 CB A:PRO87 4.9 19.9 1.0

Iodine binding site 4 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:49.0 occ:0.44 I13 A:Y6S308 0.0 49.0 0.4 C01 A:Y6S308 2.1 31.4 0.4 C06 A:Y6S308 3.1 35.1 0.4 C02 A:Y6S308 3.1 25.6 0.4 O A:HOH416 3.2 31.0 1.0 CB A:ASN112 3.7 21.5 1.0 CG A:ASN112 4.0 31.2 1.0 ND2 A:ASN112 4.0 31.2 1.0 NE A:ARG98 4.3 32.2 1.0 CD A:LYS110 4.3 49.1 1.0 CZ A:ARG98 4.5 31.4 1.0 CB A:LYS110 4.5 30.8 1.0 CB A:ALA21 4.5 25.2 1.0 C05 A:Y6S308 4.5 35.2 0.4 OD1 A:ASN112 4.6 23.7 1.0 NH2 A:ARG98 4.6 35.2 1.0 C03 A:Y6S308 4.6 30.6 0.4 CD A:ARG98 4.8 28.4 1.0 O A:MET22 4.8 17.9 1.0 CA A:ASN112 4.9 17.6 1.0 O A:HOH447 4.9 45.7 1.0

Iodine binding site 5 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:43.2 occ:0.65 I13 B:Y6S305 0.0 43.2 0.7 C01 B:Y6S305 2.1 25.5 0.7 C06 B:Y6S305 3.1 32.6 0.7 C02 B:Y6S305 3.2 24.2 0.7 CD2 B:LEU79 3.8 21.4 1.0 I13 B:Y6S307 3.9 104.0 0.6 CD2 B:PHE85 4.0 23.1 1.0 CE2 A:PHE85 4.1 27.6 1.0 CD B:ARG77 4.3 45.8 1.0 CB B:ARG77 4.4 28.6 1.0 C02 A:Y6S307 4.5 36.7 0.6 C05 B:Y6S305 4.5 34.2 0.7 CE2 B:PHE85 4.6 25.1 1.0 CZ A:PHE85 4.6 19.8 1.0 C03 B:Y6S305 4.6 38.3 0.7 CB A:PRO87 4.7 19.9 1.0 C01 A:Y6S307 4.7 48.7 0.6 I13 A:Y6S307 4.9 103.3 0.6 CG B:PHE85 4.9 16.8 1.0 CG B:ARG77 5.0 38.1 1.0

Iodine binding site 6 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:I306 b:130.9 occ:0.71 I13 B:Y6S306 0.0 130.9 0.7 C01 B:Y6S306 2.1 53.3 0.7 C02 B:Y6S306 3.1 57.9 0.7 C06 B:Y6S306 3.2 17.6 0.7 CG B:GLN100 3.5 48.3 1.0 CG B:GLU108 3.8 64.1 1.0 CD B:GLN100 4.0 55.0 1.0 C B:ALA101 4.1 34.9 1.0 N B:MET102 4.2 37.2 1.0 CB B:MET102 4.2 49.8 1.0 O B:ALA101 4.2 34.9 1.0 N B:ALA101 4.4 26.8 1.0 NE2 B:GLN100 4.4 60.0 1.0 OE1 B:GLN100 4.5 60.8 1.0 CB B:GLU108 4.5 55.0 1.0 C B:GLN100 4.6 25.4 1.0 CA B:ALA101 4.6 33.4 1.0 OE2 B:GLU108 4.6 71.2 1.0 C05 B:Y6S306 4.6 29.4 0.7 C03 B:Y6S306 4.6 60.2 0.7 CD B:GLU108 4.6 73.8 1.0 CA B:MET102 4.6 57.2 1.0 O B:GLN100 4.7 26.0 1.0 CB B:GLN100 4.8 32.2 1.0 O B:ARG48 4.9 32.1 1.0

Iodine binding site 7 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:I307 b:104.0 occ:0.63 I13 B:Y6S307 0.0 104.0 0.6 C01 B:Y6S307 2.1 52.0 0.6 C06 B:Y6S307 3.1 59.8 0.6 C02 B:Y6S307 3.2 48.4 0.6 NE B:ARG77 3.6 45.5 1.0 CD B:ARG77 3.7 45.8 1.0 O B:ASP73 3.7 30.4 1.0 I13 B:Y6S305 3.9 43.2 0.7 CG B:ARG77 4.0 38.1 1.0 CD B:PRO87 4.1 24.6 1.0 CB B:ARG77 4.1 28.6 1.0 CZ B:ARG77 4.2 56.1 1.0 CG B:PRO87 4.3 30.2 1.0 CD2 B:PHE85 4.3 23.1 1.0 CE2 B:PHE85 4.5 25.1 1.0 C05 B:Y6S307 4.5 58.2 0.6 C03 B:Y6S307 4.6 54.2 0.6 N B:ARG77 4.6 17.8 1.0 NH2 B:ARG77 4.7 40.1 1.0 O B:PHE85 4.8 13.3 1.0 NH1 B:ARG77 4.8 45.1 1.0 I13 A:Y6S306 4.9 61.6 1.0 C B:ASP73 4.9 40.5 1.0

Iodine binding site 8 out of 8 in the Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Receptor For Advanced Glycation End Products VC1 Domain in Complex with 3-(3-(((3-(4-Carboxyphenoxy)Benzyl)Oxy)Methyl)Phenyl)-1H-Indole- 2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:I308 b:37.0 occ:0.39 I13 B:Y6S308 0.0 37.0 0.4 C01 B:Y6S308 2.1 34.0 0.4 C06 B:Y6S308 3.1 23.7 0.4 C02 B:Y6S308 3.1 35.8 0.4 CB B:ASN112 3.8 20.1 1.0 CG B:ASN112 4.0 31.1 1.0 NE B:ARG98 4.0 35.0 1.0 ND2 B:ASN112 4.2 30.1 1.0 CZ B:ARG98 4.2 29.9 1.0 CD B:ARG98 4.3 29.1 1.0 CD B:LYS110 4.3 47.2 1.0 CB B:LYS110 4.4 31.5 1.0 OD1 B:ASN112 4.5 20.8 1.0 C05 B:Y6S308 4.5 27.6 0.4 NH2 B:ARG98 4.6 30.6 1.0 C03 B:Y6S308 4.6 42.2 0.4 NH1 B:ARG98 4.7 20.2 1.0 CB B:ALA21 4.7 25.1 1.0 O B:SER111 4.8 22.8 1.0 CA B:ASN112 4.9 17.6 1.0 CG B:LYS110 4.9 34.6 1.0 CG B:ARG98 4.9 25.6 1.0

N.Kozlyuk, B.A.Gilston, L.E.Salay, R.D.Gogliotti, P.P.Christov, K.Kim, M.Ovee, A.G.Waterson, W.J.Chazin. A Fragment-Based Approach to Discovery of Receptor For Advanced Glycation End Products Inhibitors. Proteins V. 89 1399 2021.
ISSN: ESSN 1097-0134
PubMed: 34156100
DOI: 10.1002/PROT.26162