Receptor
PDB id Resolution Class Description Source Keywords
1X06 1.9 Å EC: 2.5.1.31 CRYSTAL STRUCTURE OF UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MG, IPP AND FSPP ESCHERICHIA COLI ENZYME-SUBSTRATE COMPLEX METAL COORDINATION TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM, ISOPENTENYL PYROPHOSPHATE, AND FARNESYL THIOPYROPHOSPHATE: ROLES OF THE METAL ION AND CONSERVED RESIDUES IN CATALYSIS. J.BIOL.CHEM. V. 280 20762 200
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FPS A:901;
A:902;
Valid;
Valid;
none;
none;
submit data
398.392 C15 H28 O6 P2 S CC(=C...
MG A:900;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PO4 A:903;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 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 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
15 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
16 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
17 6IME - GST C10 H20 O6 P2 S CC(=CCCC(=....
18 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
19 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
20 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
21 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
22 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
23 4U82 ic50 = 1.9 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
24 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
25 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
26 6SZG - M2K C8 H10 N2 O2 C1CCc2c(c(....
27 6ACS - CIT C6 H8 O7 C(C(=O)O)C....
28 6SZH - M2H C7 H8 N2 Cc1cc([nH]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FPS; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 GGS 1 1
2 FPS 1 1
3 GST 0.911111 0.975
4 AG8 0.701754 0.816327
5 DST 0.5625 0.85
6 OTP 0.551724 0.860465
7 ZTP 0.551724 0.860465
8 VTP 0.551724 0.860465
9 FPP 0.551724 0.880952
10 GRG 0.551724 0.880952
11 0K3 0.54717 0.790698
12 FJP 0.54717 0.809524
13 DSL 0.54717 0.790698
14 HZZ 0.490566 0.785714
15 GPP 0.482759 0.857143
16 FFF 0.476923 0.822222
17 FHP 0.473684 0.704545
18 FGG 0.469697 0.822222
19 ELR 0.455882 0.840909
20 ELU 0.455882 0.840909
21 2CF 0.454545 0.822222
22 FPF 0.454545 0.822222
23 MGM 0.449275 0.685185
24 3E9 0.441176 0.840909
25 FPQ 0.426471 0.734694
26 FII 0.41791 0.6
27 PS7 0.405063 0.804348
28 749 0.403509 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: FPS; 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 : 3WYJ; Ligand: H78; 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: 3wyj.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback