Receptor
PDB id Resolution Class Description Source Keywords
4ONC 1.83 Å EC: 2.5.1.31 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DECAPRENYL D SYNTHASE IN COMPLEX WITH BPH-640 MYCOBACTERIUM TUBERCULOSIS POLYPRENYL TRANSFERASE DECAPRENYL DIPHOSPHATE SYNTHASE TRA
Ref.: STRUCTURE AND INHIBITION OF TUBERCULOSINOL SYNTHASE DECAPRENYL DIPHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS J.AM.CHEM.SOC. V. 136 2892 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
40B A:500;
B:500;
Valid;
Valid;
none;
none;
Kd = 410 nM
420.29 C19 H18 O7 P2 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ONC 1.83 Å EC: 2.5.1.31 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DECAPRENYL D SYNTHASE IN COMPLEX WITH BPH-640 MYCOBACTERIUM TUBERCULOSIS POLYPRENYL TRANSFERASE DECAPRENYL DIPHOSPHATE SYNTHASE TRA
Ref.: STRUCTURE AND INHIBITION OF TUBERCULOSINOL SYNTHASE DECAPRENYL DIPHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS J.AM.CHEM.SOC. V. 136 2892 2014
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
2 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
3 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
2 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
3 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
14 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
15 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
16 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
17 5HC7 - DST C5 H14 O6 P2 S CC(C)CCS[P....
18 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
19 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
20 4U82 ic50 = 0.39 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
21 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
22 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 40B; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 40B 1 1
2 B08 0.517241 0.852941
3 B76 0.47619 0.707317
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ONC; Ligand: 40B; Similar sites found: 9
This union binding pocket(no: 1) in the query (biounit: 4onc.bio1) has 50 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CQL NAG 0.02178 0.41569 1.23457
2 3AJ6 NGA 0.02257 0.42228 2.8169
3 3MBI HSX 0.03313 0.40195 4.57746
4 4OWK NGA 0.04989 0.40261 5.07246
5 5CSM TRP 0.01068 0.43204 7.03125
6 1M2Z BOG 0.01193 0.42502 7.39437
7 4LO2 GAL BGC 0.004417 0.46654 12.3239
8 2J5V PCA 0.008558 0.46111 12.6761
9 1HGX 5GP 0.02655 0.40696 14.7541
Pocket No.: 2; Query (leader) PDB : 4ONC; Ligand: 40B; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4onc.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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