Receptor
PDB id Resolution Class Description Source Keywords
5ESU 2.2 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND BOUND TO MG2+ AND INTERMEDIATE II (A THDP + DE-CARBOXYLATED 2-OXOGLUTARATE + I SOCHORISMATE ADDUCT) 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:603;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S C(CS)...
TOI D:602;
C:601;
Valid;
Valid;
none;
none;
submit data
753.586 C26 H35 N4 O16 P2 S [H]/N...
FMT B:601;
A:602;
Invalid;
Invalid;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
MG A:601;
C:602;
D:601;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
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: TOI; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 TOI 1 1
2 S6P TDP 0.429577 0.873563
Similar Ligands (3D)
Ligand no: 1; Ligand: TOI; Similar ligands found: 0
No: Ligand Similarity coefficient
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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