Receptor
PDB id Resolution Class Description Source Keywords
4MW1 2.49 Å EC: 6.1.1.10 TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH 1-{3-[(3-CHLORO-5-METHOXYBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-( CHEM 1444) TRYPANOSOMA BRUCEI AMINOACYL-TRNA SYNTHETASE AARS METRS PARASITE PROTEIN-INCOMPLEX ROSSMANN FOLD TRANSLATION NUCLEOTIDE BINDING LILIGASE INHIBITOR COMPLEX
Ref.: STRUCTURES OF TRYPANOSOMA BRUCEI METHIONYL-TRNA SYN WITH UREA-BASED INHIBITORS PROVIDE GUIDANCE FOR DRU AGAINST SLEEPING SICKNESS. PLOS NEGL TROP DIS V. 8 E2775 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:805;
A:802;
A:803;
B:801;
B:805;
B:803;
B:804;
A:804;
B:802;
A:801;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
44F B:808;
 Valid;
 none;
 submit data
353.867 C16 H20 Cl N3 O2 S COc1c...
DMS B:806;
B:807;
A:806;
A:807;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5V49 2.3 Å EC: 6.1.1.10 TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH (CHEM 1917) TRYPANOSOMA BRUCEI BRUCEI SYNTHETASE LIGASE METHIONINE INHIBITOR LIGASE-LIGASE INHCOMPLEX
Ref.: OPTIMIZATION OF A BINDING FRAGMENT TARGETING THE "E METHIONINE POCKET" LEADS TO POTENT TRYPANOSOMA BRUC METHIONYL-TRNA SYNTHETASE INHIBITORS. BIOORG. MED. CHEM. LETT. V. 27 2702 2017
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4ZT4 - 4RO C16 H15 Cl2 F2 N5 c1cc2c(nc1....
2 4MW1 - 44F C16 H20 Cl N3 O2 S COc1cc(cc(....
3 4MWE - 2EN C21 H26 Cl N3 O2 S C=CCc1cc(c....
4 4ZT5 - 4RN C17 H19 Cl2 N5 C[C@@H](CN....
5 4ZT7 - 4RC C18 H19 Cl2 F N6 c1cc(nc2c1....
6 4MVY - 387 C17 H19 Cl2 N3 O2 c1cc(cc(c1....
7 5J59 ic50 < 50 nM N93 C16 H16 Cl3 N5 CN(CCNCc1c....
8 4MWB - 2EK C13 H15 Cl2 N3 O S2 c1cscc1NC(....
9 5V49 ic50 < 50 nM 8WA C18 H19 Cl3 N6 CN(CCN[C@@....
10 4MW0 - 392 C17 H19 Cl2 N3 O2 c1ccc(c(c1....
11 4MW5 - 415 C18 H22 Cl N3 O2 COc1cc(cc(....
12 4ZT6 - 4RD C18 H18 Cl2 F N5 O c1cc(nc2c1....
13 4MW4 - MET C5 H11 N O2 S CSCC[C@@H]....
14 4MW2 - MET C5 H11 N O2 S CSCC[C@@H]....
15 4MWD - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4ZT4 - 4RO C16 H15 Cl2 F2 N5 c1cc2c(nc1....
2 4MW1 - 44F C16 H20 Cl N3 O2 S COc1cc(cc(....
3 4MWE - 2EN C21 H26 Cl N3 O2 S C=CCc1cc(c....
4 4ZT5 - 4RN C17 H19 Cl2 N5 C[C@@H](CN....
5 4ZT7 - 4RC C18 H19 Cl2 F N6 c1cc(nc2c1....
6 4MVY - 387 C17 H19 Cl2 N3 O2 c1cc(cc(c1....
7 5J59 ic50 < 50 nM N93 C16 H16 Cl3 N5 CN(CCNCc1c....
8 4MWB - 2EK C13 H15 Cl2 N3 O S2 c1cscc1NC(....
9 5V49 ic50 < 50 nM 8WA C18 H19 Cl3 N6 CN(CCN[C@@....
10 4MW0 - 392 C17 H19 Cl2 N3 O2 c1ccc(c(c1....
11 4MW5 - 415 C18 H22 Cl N3 O2 COc1cc(cc(....
12 4ZT6 - 4RD C18 H18 Cl2 F N5 O c1cc(nc2c1....
13 4MW4 - MET C5 H11 N O2 S CSCC[C@@H]....
14 4MW2 - MET C5 H11 N O2 S CSCC[C@@H]....
15 4MWD - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
16 6SWX ic50 = 2.06 uM LWN C15 H14 F2 N6 O2 Cn1c2c(cn1....
17 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2X1L - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 4ZT4 - 4RO C16 H15 Cl2 F2 N5 c1cc2c(nc1....
3 4MW1 - 44F C16 H20 Cl N3 O2 S COc1cc(cc(....
4 4MWE - 2EN C21 H26 Cl N3 O2 S C=CCc1cc(c....
5 4ZT5 - 4RN C17 H19 Cl2 N5 C[C@@H](CN....
6 4ZT7 - 4RC C18 H19 Cl2 F N6 c1cc(nc2c1....
7 4MVY - 387 C17 H19 Cl2 N3 O2 c1cc(cc(c1....
8 5J59 ic50 < 50 nM N93 C16 H16 Cl3 N5 CN(CCNCc1c....
9 4MWB - 2EK C13 H15 Cl2 N3 O S2 c1cscc1NC(....
10 5V49 ic50 < 50 nM 8WA C18 H19 Cl3 N6 CN(CCN[C@@....
11 4MW0 - 392 C17 H19 Cl2 N3 O2 c1ccc(c(c1....
12 4MW5 - 415 C18 H22 Cl N3 O2 COc1cc(cc(....
13 4ZT6 - 4RD C18 H18 Cl2 F N5 O c1cc(nc2c1....
14 4MW4 - MET C5 H11 N O2 S CSCC[C@@H]....
15 4MW2 - MET C5 H11 N O2 S CSCC[C@@H]....
16 4MWD - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
17 6SWX ic50 = 2.06 uM LWN C15 H14 F2 N6 O2 Cn1c2c(cn1....
18 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
19 5K0S ic50 = 0.006 uM 0OU C19 H19 Cl2 N3 O c1ccc2c(c1....
20 4PY2 ic50 = 0.272 uM 43E C15 H17 Cl2 N3 O S c1cscc1NC(....
21 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 44F; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 44F 1 1
2 43E 0.73913 0.857143
3 415 0.72 0.894737
4 2EK 0.556962 0.766667
5 2EB 0.523256 0.868852
6 2E9 0.516854 0.854839
7 2EN 0.5 0.870968
8 387 0.470588 0.813559
9 392 0.447059 0.774194
Similar Ligands (3D)
Ligand no: 1; Ligand: 44F; Similar ligands found: 5
No: Ligand Similarity coefficient
1 4RN 0.9156
2 N93 0.9088
3 0OU 0.8808
4 8WA 0.8753
5 4RO 0.8611
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5V49; Ligand: MET; 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: 5v49.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5V49; Ligand: 8WA; 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: 5v49.bio2) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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