Iodine in PDB 8ovz: Crystal Structure of D1228V C-Met Bound By Compound 16

All present enzymatic activity of Crystal Structure of D1228V C-Met Bound By Compound 16:
2.7.10.1;

The structure of Crystal Structure of D1228V C-Met Bound By Compound 16, PDB code: 8ovz was solved by G.W.Collie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.08 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.9, 56.67, 215.81, 90, 90, 90
R / Rfree (%)	22.5 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of D1228V C-Met Bound By Compound 16 (pdb code 8ovz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of D1228V C-Met Bound By Compound 16, PDB code: 8ovz:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1401 b:61.6 occ:1.00 N A:ALA1226 3.4 38.7 1.0 CB A:ARG1114 3.9 60.4 1.0 CB A:ALA1226 3.9 38.8 1.0 CD2 A:LEU1225 4.0 42.0 1.0 CA A:LEU1225 4.1 39.5 1.0 CB A:PHE1089 4.1 47.6 1.0 CA A:PHE1089 4.2 47.7 1.0 CD A:ARG1114 4.2 67.5 1.0 C A:LEU1225 4.3 39.4 1.0 CA A:ALA1226 4.3 38.7 1.0 CB A:LEU1225 4.4 40.1 1.0 CD2 A:LEU1112 4.4 50.9 1.0 CG A:ARG1114 4.4 64.0 1.0 O A:PHE1089 4.5 47.6 1.0 N A:ARG1114 4.5 57.4 1.0 CB A:LEU1112 4.7 48.9 1.0 CA A:ARG1114 4.7 58.9 1.0 O A:HOH1533 4.7 51.0 1.0 CG1 A:ILE1115 4.8 62.7 1.0 CG A:LEU1225 4.9 41.4 1.0 CA A:LEU1112 4.9 48.9 1.0 C A:PHE1089 4.9 47.4 1.0 C A:LEU1112 5.0 50.9 1.0

Iodine binding site 2 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1402 b:117.1 occ:1.00 OG1 A:THR1096 3.7 50.4 1.0 CB A:HIS1106 3.7 44.2 1.0 CA A:HIS1106 3.9 43.9 1.0 CG A:HIS1106 4.0 46.5 1.0 N A:HIS1106 4.1 44.9 1.0 CG2 A:THR1096 4.3 48.9 1.0 CD2 A:HIS1106 4.4 47.2 1.0 CB A:LYS1104 4.4 52.0 1.0 CB A:THR1096 4.5 48.7 1.0 C A:ILE1105 4.5 46.6 1.0 O A:ILE1105 4.6 46.8 1.0 O A:GLY1095 4.7 43.2 1.0 CD A:LYS1104 4.7 59.3 1.0 ND1 A:HIS1106 4.7 48.2 1.0 CA A:THR1096 4.9 46.6 1.0 O A:HOH1580 5.0 62.9 1.0

Iodine binding site 3 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1403 b:36.1 occ:0.50 O A:HOH1511 3.3 29.8 1.0 CA A:TYR1194 3.9 27.4 1.0 N A:TYR1194 4.2 27.7 1.0 CB A:TYR1194 4.2 26.7 1.0 CG A:LYS1193 4.3 26.7 1.0 CD1 A:TYR1194 4.3 28.0 1.0 CE A:LYS1193 4.3 34.0 1.0 NE2 A:HIS1136 4.5 30.0 1.0 C A:LYS1193 4.5 27.3 1.0 CD A:LYS1193 4.5 30.2 1.0 CD2 A:HIS1136 4.5 28.8 1.0 O A:LYS1193 4.6 27.8 1.0 CG A:TYR1194 4.8 27.2 1.0 OG A:SER1197 4.8 33.2 1.0

Iodine binding site 4 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1404 b:31.1 occ:0.50 NZ A:LYS1318 3.8 47.5 1.0 CB A:ARG1336 3.9 35.2 1.0 CB A:PRO1328 3.9 32.7 1.0 CG A:ARG1336 4.0 37.7 1.0 CG A:PRO1328 4.1 33.4 1.0 CD A:LYS1318 4.2 42.5 1.0 CE A:LYS1318 4.2 45.9 1.0 CG2 A:VAL1315 4.3 30.5 1.0 CD2 A:LEU1333 4.4 34.5 1.0 O A:GLU1332 4.6 32.0 1.0 CG1 A:VAL1315 4.8 32.0 1.0 C A:GLU1332 4.8 32.0 1.0 O A:HOH1560 4.8 40.4 1.0 CB A:GLU1332 4.8 35.5 1.0 OE2 A:GLU1332 4.8 52.1 1.0 CB A:VAL1315 4.9 31.2 1.0 CA A:LEU1333 4.9 31.8 1.0 N A:LEU1333 5.0 31.7 1.0 CD A:ARG1336 5.0 42.0 1.0

Iodine binding site 5 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1405 b:36.8 occ:0.50 O A:HOH1522 3.0 39.9 1.0 CA A:GLY1072 4.0 39.7 1.0 N A:GLY1072 4.3 39.2 1.0 O A:HOH1526 4.3 46.8 1.0 C A:ILE1071 4.7 39.5 1.0 CG1 A:VAL1070 4.7 36.5 1.0 O A:ILE1071 4.8 39.6 1.0 CD A:PRO1073 4.9 39.6 1.0

Iodine binding site 6 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1406 b:36.3 occ:0.50 O A:HOH1525 3.1 46.4 1.0 N A:LYS1248 3.7 32.6 1.0 CG A:LYS1248 3.7 33.3 1.0 N A:VAL1247 3.9 35.0 1.0 CB A:LYS1248 3.9 31.6 1.0 CZ3 A:TRP1249 4.0 29.1 1.0 OG1 A:THR1289 4.1 46.0 1.0 O A:LEU1245 4.1 39.9 1.0 CD A:LYS1248 4.2 36.2 1.0 C A:PRO1246 4.3 35.9 1.0 CE3 A:TRP1249 4.3 29.0 1.0 CA A:LYS1248 4.4 31.6 1.0 CB A:VAL1247 4.5 34.8 1.0 CA A:PRO1246 4.5 36.8 1.0 CA A:VAL1247 4.5 34.5 1.0 C A:VAL1247 4.6 33.6 1.0 CE A:LYS1248 4.6 38.4 1.0 O A:PRO1246 5.0 36.1 1.0

Iodine binding site 7 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1407 b:54.3 occ:0.50 N A:HIS1088 3.6 46.9 1.0 CB A:HIS1088 3.8 49.8 1.0 CA A:GLY1224 3.9 38.7 1.0 CD1 A:PHE1089 4.0 49.4 1.0 O A:PHE1223 4.0 40.4 1.0 CA A:HIS1088 4.3 48.0 1.0 ND1 A:HIS1088 4.3 56.3 1.0 CE1 A:PHE1089 4.4 50.1 1.0 CG A:HIS1088 4.5 53.7 1.0 C A:GLY1224 4.5 38.8 1.0 O A:HOH1563 4.5 39.9 1.0 C A:GLY1087 4.6 46.4 1.0 CA A:GLY1087 4.6 46.0 1.0 N A:PHE1089 4.6 47.7 1.0 N A:LEU1225 4.7 39.0 1.0 C A:PHE1223 4.9 38.9 1.0 N A:GLY1224 4.9 38.5 1.0 C A:HIS1088 4.9 48.3 1.0

Iodine binding site 8 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1408 b:63.2 occ:0.50 N A:MET1229 3.4 42.0 1.0 CB A:MET1229 3.7 45.6 1.0 N A:TYR1230 3.8 42.5 1.0 CG A:GLU1233 3.8 57.0 1.0 CD2 A:TYR1230 3.8 46.0 1.0 OE1 A:GLN1123 3.9 61.1 1.0 CG A:GLN1123 3.9 49.4 1.0 CA A:MET1229 4.0 43.6 1.0 CD A:GLN1123 4.0 57.7 1.0 CB A:GLU1233 4.1 49.1 1.0 CB A:VAL1228 4.2 41.2 1.0 C A:MET1229 4.4 43.5 1.0 C A:VAL1228 4.4 41.2 1.0 CE2 A:TYR1230 4.5 47.1 1.0 CA A:VAL1228 4.5 40.1 1.0 CG A:TYR1230 4.5 44.6 1.0 CB A:TYR1230 4.6 42.8 1.0 CD A:GLU1233 4.7 67.3 1.0 CB A:GLN1123 4.7 44.1 1.0 CA A:TYR1230 4.8 42.1 1.0 CG1 A:VAL1228 4.8 42.0 1.0 NE2 A:GLN1123 4.9 58.5 1.0 OE2 A:GLU1233 5.0 70.4 1.0

Iodine binding site 9 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1409 b:66.0 occ:0.50 O A:HOH1535 3.1 39.1 1.0 N A:SER1141 3.4 31.3 1.0 CG A:PRO1158 3.5 34.4 1.0 OG A:SER1141 3.7 36.4 1.0 CB A:SER1141 3.7 33.6 1.0 CE A:LYS1219 3.8 44.0 1.0 NZ A:LYS1219 3.8 45.0 1.0 CD1 A:LEU1140 4.1 27.2 1.0 CA A:SER1141 4.2 32.0 1.0 CB A:PRO1158 4.2 34.2 1.0 O A:VAL1139 4.2 28.1 1.0 CA A:LEU1140 4.2 29.4 1.0 CD A:LYS1219 4.2 41.1 1.0 C A:LEU1140 4.3 30.9 1.0 CD A:PRO1158 4.6 33.0 1.0 CE A:MET1160 4.7 39.3 1.0 CG A:LYS1219 4.8 38.0 1.0 CG A:LEU1140 5.0 28.0 1.0 C A:VAL1139 5.0 28.8 1.0

Iodine binding site 10 out of 19 in the Crystal Structure of D1228V C-Met Bound By Compound 16


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 D1228V C-Met Bound By Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1410 b:63.1 occ:0.50 O A:HOH1573 3.5 40.5 1.0 N A:LYS1232 3.6 42.8 1.0 N A:ASP1231 3.8 40.2 1.0 CB A:TYR1230 3.9 42.8 1.0 CB A:LYS1232 4.0 45.3 1.0 CE A:LYS1259 4.1 58.5 1.0 CB A:ASP1231 4.3 42.0 1.0 CA A:ASP1231 4.4 40.8 1.0 CA A:LYS1232 4.4 43.8 1.0 CD1 A:TYR1230 4.4 46.2 1.0 C A:ASP1231 4.4 42.0 1.0 C A:TYR1230 4.4 40.8 1.0 CA A:TYR1230 4.4 42.1 1.0 CG A:TYR1230 4.5 44.6 1.0 CD A:LYS1259 4.7 53.9 1.0 NZ A:LYS1259 4.8 61.2 1.0 O A:HOH1527 4.8 39.4 1.0 CG A:ASP1231 5.0 46.4 1.0

I.N.Michaelides, G.W.Collie, U.Borjesson, C.Vasalou, O.Alkhatib, L.Barlind, T.Cheung, I.L.Dale, K.J.Embrey, E.J.Hennessy, P.Khurana, C.M.Koh, M.L.Lamb, J.Liu, T.A.Moss, D.J.O'neill, C.Phillips, J.Shaw, A.Snijder, R.I.Storer, C.J.Stubbs, F.Han, C.Li, J.Qiao, D.Q.Sun, J.Wang, P.Wang, W.Yang. Discovery and Optimization of the First Atp Competitive Type-III C-Met Inhibitor. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37343272
DOI: 10.1021/ACS.JMEDCHEM.3C00401