Receptor
PDB id Resolution Class Description Source Keywords
5ESD 2.25 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND BOUND TO THDP AND MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MENAQUINONE BIOSYNTHESIS MEND 2-SUCCINYL-5-ENOLPYRUVYL-6-HCYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE THIAMIN-DIPHOSPHATE ENZYME PYRUVATE OXIDASE FAMILY HYDROLASE
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
MN C:602;
D:602;
B:602;
A:601;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
54.938 Mn [Mn+2...
TDP B:601;
D:601;
C:601;
A:602;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
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 (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6O0J - DNA C11 H8 O4 c1ccc2c(c1....
2 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
3 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
4 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
5 6O0G - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
6 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
7 6O04 - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6O0J - DNA C11 H8 O4 c1ccc2c(c1....
2 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
3 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
4 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
5 6O0G - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
6 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
7 6O04 - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6O0J - DNA C11 H8 O4 c1ccc2c(c1....
2 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
3 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
4 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
5 6O0G - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
6 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
7 6O04 - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TDP; Similar ligands found: 34
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 NDQ 0.647059 0.896104
9 2TP 0.609195 0.918919
10 VIB 0.605263 0.760563
11 5SR 0.582418 0.958333
12 FTP 0.574713 0.847222
13 O2T 0.546392 0.896104
14 PYI 0.483871 0.873239
15 HTL 0.474227 0.945205
16 TDW 0.474227 0.958333
17 AUJ 0.47 0.907895
18 THV 0.46 0.945205
19 TD6 0.457143 0.907895
20 WWF 0.455446 0.92
21 TOG 0.451923 0.907895
22 TPW 0.451613 0.885714
23 THY 0.45098 0.932432
24 TD9 0.448598 0.907895
25 TD8 0.448598 0.907895
26 THW 0.447619 0.945205
27 TDL 0.446602 0.884615
28 TDK 0.442308 0.907895
29 D7K 0.415929 0.896104
30 TPU 0.410526 0.828947
31 S1T 0.405941 0.873239
32 R1T 0.405941 0.873239
33 T6F 0.403509 0.884615
34 T5X 0.403509 0.884615
Similar Ligands (3D)
Ligand no: 1; Ligand: TDP; Similar ligands found: 14
No: Ligand Similarity coefficient
1 TZD 0.9840
2 TP9 0.9719
3 8EO 0.9703
4 8EL 0.9688
5 8EF 0.9680
6 DPX 0.9588
7 8FL 0.9547
8 HTD 0.9474
9 G8G 0.9423
10 TDM 0.9227
11 1U0 0.8889
12 THD 0.8812
13 8N9 0.8650
14 TDN 0.8521
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5eso.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
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