Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:802;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
MET A:800;
 Valid;
 none;
 submit data
149.211 C5 H11 N O2 S CSCC[...
8WA B:801;
 Valid;
 none;
 ic50 < 50 nM
425.743 C18 H19 Cl3 N6 CN(CC...
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 (16)
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 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
50% Homology Family (20)
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 5K0S ic50 = 0.006 uM 0OU C19 H19 Cl2 N3 O c1ccc2c(c1....
18 4PY2 ic50 = 0.272 uM 43E C15 H17 Cl2 N3 O S c1cscc1NC(....
19 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
20 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MED 1 1
2 MET 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 MF3 0.5 0.647059
7 NVA 0.5 0.758621
8 HSE 0.466667 0.617647
9 DAB 0.466667 0.636364
10 MHO 0.457143 0.717949
11 SME 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 DGL 0.424242 0.625
22 GGL 0.424242 0.625
23 GLU 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 FME 0.410256 0.84375
27 AME 0.410256 0.771429
28 LEU 0.40625 0.666667
29 JM6 0.4 0.7
30 CYS 0.4 0.666667
31 DCY 0.4 0.666667
32 C2N 0.4 0.633333
Ligand no: 2; Ligand: 8WA; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 8WA 1 1
2 N93 0.473118 0.931035
3 4RC 0.409091 0.833333
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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