Receptor
PDB id Resolution Class Description Source Keywords
5ESO 2.05 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND WITH THDP, MG2+ AN ISOCHORISMATE BOUND MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MENAQUINONE BIOSYNTHESIS MEND 2-SUCCINYL-5-ENOLPYRUVYL-6-HCYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE THIAMIN-DIPHOSPHATE ENZYME PYRUVATE OXIDASE FAMILY TRANSFERASE
Ref.: STRUCTURAL VIEWS ALONG THE MYCOBACTERIUM TUBERCULOS REACTION PATHWAY ILLUMINATE KEY ASPECTS OF THIAMIN DIPHOSPHATE-DEPENDENT ENZYME MECHANISMS. STRUCTURE V. 24 1167 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME D:603;
C:606;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S C(CS)...
ISC B:602;
A:602;
Valid;
Valid;
none;
none;
submit data
226.183 C10 H10 O6 C=C(C...
MG B:601;
D:601;
A:601;
C:601;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
FMT C:604;
C:603;
A:603;
B:603;
B:604;
C:602;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
GOL B:605;
A:604;
A:605;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TDP D:602;
C:605;
Valid;
Valid;
none;
none;
submit data
424.306 C12 H18 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ESO 2.05 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND WITH THDP, MG2+ AN ISOCHORISMATE BOUND MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MENAQUINONE BIOSYNTHESIS MEND 2-SUCCINYL-5-ENOLPYRUVYL-6-HCYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE THIAMIN-DIPHOSPHATE ENZYME PYRUVATE OXIDASE FAMILY TRANSFERASE
Ref.: STRUCTURAL VIEWS ALONG THE MYCOBACTERIUM TUBERCULOS REACTION PATHWAY ILLUMINATE KEY ASPECTS OF THIAMIN DIPHOSPHATE-DEPENDENT ENZYME MECHANISMS. STRUCTURE V. 24 1167 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ISC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 ISC 1 1
2 QLI 0.55102 0.714286
Ligand no: 2; Ligand: TDP; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 TDP 1 1
2 TPP 0.84 0.985714
3 V4E 0.797468 0.985714
4 TPS 0.77027 0.942857
5 TMV 0.75 0.944444
6 VNP 0.703704 0.945205
7 N1T 0.674699 1
8 2TP 0.609195 0.918919
9 VIB 0.605263 0.760563
10 5SR 0.582418 0.958333
11 FTP 0.574713 0.847222
12 O2T 0.546392 0.896104
13 PYI 0.483871 0.873239
14 TDW 0.474227 0.958333
15 HTL 0.474227 0.945205
16 THV 0.46 0.945205
17 TD6 0.457143 0.907895
18 WWF 0.455446 0.92
19 TOG 0.451923 0.907895
20 TPW 0.451613 0.885714
21 THY 0.45098 0.932432
22 TD9 0.448598 0.907895
23 TD8 0.448598 0.907895
24 THW 0.447619 0.945205
25 TDL 0.446602 0.884615
26 TDK 0.442308 0.907895
27 D7K 0.415929 0.896104
28 TPU 0.410526 0.828947
29 R1T 0.405941 0.873239
30 S1T 0.405941 0.873239
31 T6F 0.403509 0.884615
32 T5X 0.403509 0.884615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4A59 AMP 0.01527 0.40204 1.21951
2 1ZPD DPX 0.000000008068 0.57341 1.23239
3 4ZOW CLM 0.01654 0.40046 1.79028
4 2C42 PYR 0.000009062 0.47493 1.91638
5 2C42 TPP 0.000009062 0.47493 1.91638
6 5TME UDP 0.01837 0.41831 1.92719
7 1NLM UD1 0.0126 0.41208 2.1978
8 1R9J TPP 0.001081 0.44284 2.26481
9 5B48 TDN 0.000003326 0.52053 2.43902
10 2VF7 ADP 0.0302 0.4036 2.43902
11 1R2J FAD 0.02553 0.40066 2.45902
12 2DE4 BPS 0.02529 0.4075 2.46575
13 4YDS ATP 0.0199 0.42477 2.63158
14 3BRE C2E 0.03705 0.41073 3.07263
15 3LL5 IP8 0.04995 0.40249 3.21285
16 3IT7 TLA 0.02192 0.41899 3.2967
17 2VK4 TPP 0.00000001278 0.63819 3.37478
18 4PPF FLC 0.01604 0.43204 3.42857
19 3B5J 12D 0.03835 0.40924 3.7037
20 1QPB PYM 0.000000009845 0.56063 3.73002
21 1QPB TPP 0.00000002176 0.54952 3.73002
22 4NV0 MG7 0.0277 0.4055 3.76176
23 2YIC TPP 0.004285 0.4063 3.83275
24 2NSX IFM 0.029 0.40449 4.00697
25 1UMD TDP COI 0.0005137 0.44944 4.01235
26 2QV7 ADP 0.01798 0.40801 4.74777
27 4OFG PCG 0.01216 0.42353 4.86111
28 1W6F ISZ 0.006823 0.44935 5.03597
29 5AGR A52 0.01944 0.40637 5.17241
30 4JCA CIT 0.01298 0.42542 5.38922
31 1G2O IMH 0.02197 0.40381 5.59701
32 3SHR CMP 0.02652 0.41005 5.68562
33 3DVA TPW 0.001235 0.43382 5.69106
34 2R0D 4IP 0.02903 0.41584 5.76369
35 3EYA TDP 0.00000001142 0.55033 6.01093
36 1LES GLC FRU 0.02379 0.42822 6.07735
37 2ACV UDP 0.00964 0.42471 6.2635
38 4R78 AMP 0.02428 0.41592 6.79612
39 3EXH TPP 0.0003926 0.46944 6.80628
40 2A5F NAD 0.01308 0.4182 7.42857
41 2VBF TPP 0.000000003538 0.58504 8.24561
42 2UZ1 TPP 0.0000000248 0.62638 8.70337
43 1UPA TPP 0.0000002441 0.58567 8.726
44 2IHT TPP 0.0000003332 0.50436 8.726
45 2W97 MGO 0.03535 0.40725 8.75576
46 2IHU TP9 0.0000001862 0.55106 8.90052
47 5EXE 5SR 0.00001402 0.49658 9.52381
48 2O66 FLC 0.03148 0.41504 9.62963
49 4QS9 BGC 0.0382 0.40546 9.70464
50 1YQT ADP 0.0159 0.43296 9.8513
51 1OZH HE3 0.000009582 0.51319 9.93031
52 5T46 MGP 0.01216 0.44191 10.6061
53 1JJ7 ADP 0.03185 0.41774 10.7692
54 4RJK TPP 0.000000353 0.56811 11.3835
55 5E5U MLI 0.02569 0.43537 12.5628
56 1T0S BML 0.0334 0.41482 13.9535
57 1T9D P22 0.000006853 0.61095 14.1115
58 1T9D PYD 0.00001985 0.56286 14.1115
59 1T9D P25 0.00000001889 0.4206 14.1115
60 1T9D FAD 0.00000002081 0.42014 14.1115
61 1T9D 1MM 0.00000002195 0.41748 14.1115
62 2NXW TPP 0.00000008758 0.57071 16.6372
Pocket No.: 2; Query (leader) PDB : 5ESO; Ligand: TDP; Similar sites found: 62
This union binding pocket(no: 2) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4A59 AMP 0.01527 0.40204 1.21951
2 1ZPD DPX 0.000000008068 0.57341 1.23239
3 4ZOW CLM 0.01654 0.40046 1.79028
4 2C42 PYR 0.000009062 0.47493 1.91638
5 2C42 TPP 0.000009062 0.47493 1.91638
6 5TME UDP 0.01837 0.41831 1.92719
7 1NLM UD1 0.0126 0.41208 2.1978
8 1R9J TPP 0.001081 0.44284 2.26481
9 5B48 TDN 0.000003326 0.52053 2.43902
10 2VF7 ADP 0.0302 0.4036 2.43902
11 1R2J FAD 0.02553 0.40066 2.45902
12 2DE4 BPS 0.02529 0.4075 2.46575
13 4YDS ATP 0.0199 0.42477 2.63158
14 3BRE C2E 0.03705 0.41073 3.07263
15 3LL5 IP8 0.04995 0.40249 3.21285
16 3IT7 TLA 0.02192 0.41899 3.2967
17 2VK4 TPP 0.00000001278 0.63819 3.37478
18 4PPF FLC 0.01604 0.43204 3.42857
19 3B5J 12D 0.03835 0.40924 3.7037
20 1QPB PYM 0.000000009845 0.56063 3.73002
21 1QPB TPP 0.00000002176 0.54952 3.73002
22 4NV0 MG7 0.0277 0.4055 3.76176
23 2YIC TPP 0.004285 0.4063 3.83275
24 2NSX IFM 0.029 0.40449 4.00697
25 1UMD TDP COI 0.0005137 0.44944 4.01235
26 2QV7 ADP 0.01798 0.40801 4.74777
27 4OFG PCG 0.01216 0.42353 4.86111
28 1W6F ISZ 0.006823 0.44935 5.03597
29 5AGR A52 0.01944 0.40637 5.17241
30 4JCA CIT 0.01298 0.42542 5.38922
31 1G2O IMH 0.02197 0.40381 5.59701
32 3SHR CMP 0.02652 0.41005 5.68562
33 3DVA TPW 0.001235 0.43382 5.69106
34 2R0D 4IP 0.02903 0.41584 5.76369
35 3EYA TDP 0.00000001142 0.55033 6.01093
36 1LES GLC FRU 0.02379 0.42822 6.07735
37 2ACV UDP 0.00964 0.42471 6.2635
38 4R78 AMP 0.02428 0.41592 6.79612
39 3EXH TPP 0.0003926 0.46944 6.80628
40 2A5F NAD 0.01308 0.4182 7.42857
41 2VBF TPP 0.000000003538 0.58504 8.24561
42 2UZ1 TPP 0.0000000248 0.62638 8.70337
43 1UPA TPP 0.0000002441 0.58567 8.726
44 2IHT TPP 0.0000003332 0.50436 8.726
45 2W97 MGO 0.03535 0.40725 8.75576
46 2IHU TP9 0.0000001862 0.55106 8.90052
47 5EXE 5SR 0.00001402 0.49658 9.52381
48 2O66 FLC 0.03148 0.41504 9.62963
49 4QS9 BGC 0.0382 0.40546 9.70464
50 1YQT ADP 0.0159 0.43296 9.8513
51 1OZH HE3 0.000009582 0.51319 9.93031
52 5T46 MGP 0.01216 0.44191 10.6061
53 1JJ7 ADP 0.03185 0.41774 10.7692
54 4RJK TPP 0.000000353 0.56811 11.3835
55 5E5U MLI 0.02569 0.43537 12.5628
56 1T0S BML 0.0334 0.41482 13.9535
57 1T9D P22 0.000006853 0.61095 14.1115
58 1T9D PYD 0.00001985 0.56286 14.1115
59 1T9D P25 0.00000001889 0.4206 14.1115
60 1T9D FAD 0.00000002081 0.42014 14.1115
61 1T9D 1MM 0.00000002195 0.41748 14.1115
62 2NXW TPP 0.00000008758 0.57071 16.6372
Pocket No.: 3; Query (leader) PDB : 5ESO; Ligand: TDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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