Receptor
PDB id Resolution Class Description Source Keywords
5CQJ 2.15 Å EC: 2.5.1.31 CRYSTAL STRUCTURE OF E. COLI UNDECAPRENYL PYROPHOSPHATE SYNT COMPLEX WITH CLOMIPHENE ESCHERICHIA COLI (STRAIN K12) TRANSFERASE CELL WALL WALL TEICHOIC ACID ANTIBACTERIAL TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: ANTAGONISM SCREEN FOR INHIBITORS OF BACTERIAL CELL BIOGENESIS UNCOVERS AN INHIBITOR OF UNDECAPRENYL DI SYNTHASE. PROC.NATL.ACAD.SCI.USA V. 112 11048 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
53Q A:301;
 Valid;
 none;
 ic50 = 15.4 uM
405.96 C26 H28 Cl N O CCN(C...
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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: 53Q; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 53Q 1 1
2 OHT 0.465753 0.782609
Similar Ligands (3D)
Ligand no: 1; Ligand: 53Q; Similar ligands found: 12
No: Ligand Similarity coefficient
1 5DJ 0.9233
2 5G7 0.9142
3 5J2 0.9133
4 5G3 0.9096
5 5G4 0.9089
6 5G5 0.9052
7 5HW 0.8903
8 P57 0.8784
9 O5E 0.8749
10 NGE 0.8672
11 SLB 0.8637
12 DAN 0.8567
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
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