Receptor
PDB id Resolution Class Description Source Keywords
2vi5 2.3 Å EC: 2.5.1.9 LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N (RIBITYLAMINO)PYRIMIDINE-2,4(1H,3H)-DIONE-5-YL-PROPIONAMIDE MYCOBACTERIUM TUBERCULOSIS TRANSFERASE LUMAZINE SYNTHASE RIBOFLAVIN BIOSYNTHESIS MYCOBACTERIUM TUBERCULOSIS
Ref.: A NEW SERIES OF N-[2,4-DIOXO-6-D-RIBITYLAMINO-1,2, 3,4-TETRAHYDROPYRIMIDIN-5-YL]OXALAMIC ACID DERIVATI INHIBITORS OF LUMAZINE SYNTASE AND RIBOFLAVIN SYNTH DESIGN, SYNTHESIS, BIOCHEMICAL EVALUATION, CRYSTALL AND MECHANISTIC IMPLICATIONS. J.ORG.CHEM.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:601;
A:603;
B:601;
B:603;
C:601;
C:603;
D:601;
D:603;
E:601;
E:603;
F:601;
G:601;
H:601;
I:601;
J:601;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
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 submit data
39.098 K [K+]
PO4 A:702;
B:702;
C:702;
D:702;
E:702;
F:702;
G:702;
H:702;
I:702;
J:702;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
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 submit data
94.971 O4 P [O-]P...
Y19 A:201;
B:201;
C:201;
D:201;
E:201;
F:201;
G:201;
H:201;
I:201;
J:201;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 Ki = 110 uM
332.31 C12 H20 N4 O7 CCC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2C94 1.9 Å EC: 2.5.1.9 LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3 TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) 1,1 DIFLUOROPP HOSPHATE MYCOBACTERIUM TUBERCULOSIS TRANSFERASE RIBOFLAVIN BIOSYNTHESIS MYCOBACTERIUM TUBERCULLUMAZINE SYNTHASE INHIBITOR BINDING
Ref.: STRUCTURAL AND THERMODYNAMIC INSIGHTS INTO THE BIND OF FIVE NOVEL INHIBITORS OF LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS. FEBS J. V. 273 4790 2006
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2C97 Ka = 1380000 M^-1 JCL C8 H12 Cl N2 O6 P C(CCOP(=O)....
2 2C94 Ka = 6540000 M^-1 TSF C15 H23 F2 N4 O10 P C(CCN1C2=C....
3 1W19 - T1P C13 H21 N4 O11 P C(CN1C2=C(....
4 2C92 Ka = 474900 M^-1 TP6 C15 H25 N4 O11 P C(CCN1C2=C....
5 2VI5 Ki = 110 uM Y19 C12 H20 N4 O7 CCC(=O)N[C....
6 1W29 - TS0 C14 H23 N4 O11 P C(CCOP(=O)....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2C97 Ka = 1380000 M^-1 JCL C8 H12 Cl N2 O6 P C(CCOP(=O)....
2 2C94 Ka = 6540000 M^-1 TSF C15 H23 F2 N4 O10 P C(CCN1C2=C....
3 1W19 - T1P C13 H21 N4 O11 P C(CN1C2=C(....
4 2C92 Ka = 474900 M^-1 TP6 C15 H25 N4 O11 P C(CCN1C2=C....
5 2VI5 Ki = 110 uM Y19 C12 H20 N4 O7 CCC(=O)N[C....
6 1W29 - TS0 C14 H23 N4 O11 P C(CCOP(=O)....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4KQ6 - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 2C97 Ka = 1380000 M^-1 JCL C8 H12 Cl N2 O6 P C(CCOP(=O)....
3 2C94 Ka = 6540000 M^-1 TSF C15 H23 F2 N4 O10 P C(CCN1C2=C....
4 1W19 - T1P C13 H21 N4 O11 P C(CN1C2=C(....
5 2C92 Ka = 474900 M^-1 TP6 C15 H25 N4 O11 P C(CCN1C2=C....
6 2VI5 Ki = 110 uM Y19 C12 H20 N4 O7 CCC(=O)N[C....
7 1W29 - TS0 C14 H23 N4 O11 P C(CCOP(=O)....
8 1NQX - RLP C14 H18 N4 O9 C(CC(=O)O)....
9 1NQU - RDL C11 H14 N4 O8 C([C@@H]([....
10 1NQW - 5YL C14 H26 N3 O9 P C(CCC1=C(N....
11 1NQV - LMZ C9 H14 N4 O7 C([C@@H]([....
12 1RVV - INI C9 H14 N4 O8 C([C@@H]([....
13 1KYV Kd = 1.2 uM RBF C17 H20 N4 O6 Cc1cc2c(cc....
14 1KYY - INI C9 H14 N4 O8 C([C@@H]([....
15 1EJB - INJ C14 H26 N3 O9 P C(CCc1c(nc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: Y19; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 Y19 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: Y19; Similar ligands found: 2
No: Ligand Similarity coefficient
1 LMZ 0.8870
2 INI 0.8744
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2C94; Ligand: TSF; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 2c94.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 2F59 INI 49.375
2 2F59 INI 49.375
3 2F59 INI 49.375
4 2F59 INI 49.375
5 2F59 INI 49.375
6 2F59 INI 49.375
Pocket No.: 2; Query (leader) PDB : 2C94; Ligand: TSF; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 2c94.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2F59 INI 49.375
2 2F59 INI 49.375
3 2F59 INI 49.375
4 2F59 INI 49.375
5 2F59 INI 49.375
6 2F59 INI 49.375
Pocket No.: 3; Query (leader) PDB : 2C94; Ligand: TSF; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 2c94.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2F59 INI 49.375
2 2F59 INI 49.375
3 2F59 INI 49.375
4 2F59 INI 49.375
Pocket No.: 4; Query (leader) PDB : 2C94; Ligand: TSF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2c94.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2C94; Ligand: TSF; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 2c94.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 2F59 INI 49.375
2 2F59 INI 49.375
3 2F59 INI 49.375
4 2F59 INI 49.375
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