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 5 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 (19)
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 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 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 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 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
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: 20
This union binding pocket(no: 1) in the query (biounit: 5v49.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1IID NHM 0.04753 0.40508 1.4218
2 3VSV XYS 0.01477 0.40313 2.58303
3 3EWR APR 0.02767 0.40202 2.97619
4 5JBX MLI 0.007468 0.40564 3.06513
5 4OAR 2S0 0.01179 0.41449 3.87597
6 2OYS FMN 0.02172 0.40285 4.05904
7 4ZOM 4Q3 0.04414 0.42564 4.88889
8 2CYC TYR 0.0109 0.40627 5.86667
9 5L92 C0R 0.02138 0.4131 6.58537
10 5L92 MLA 0.01852 0.40948 6.58537
11 2PS1 ORO 0.009633 0.40382 7.07965
12 2CYB TYR 0.008237 0.41123 7.73994
13 3FUU ADN 0.02183 0.40108 8.11808
14 3ZIU LSS 0.0001979 0.50908 8.30258
15 5L7G 6QE 0.01939 0.40693 9.18033
16 3KFC 61X 0.04185 0.40124 9.48617
17 5B4B LP5 0.02545 0.41037 10.8871
18 2V0C LEU LMS 0.0001202 0.40764 13.4686
19 2DX7 CIT 0.007876 0.41525 13.5965
20 4A91 GLU 0.0001731 0.48203 15.7718
Pocket No.: 2; Query (leader) PDB : 5V49; Ligand: 8WA; Similar sites found: 34
This union binding pocket(no: 2) in the query (biounit: 5v49.bio2) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3E5P PPI 0.0141 0.44193 2.15633
2 3VSV XYS 0.04813 0.40408 2.58303
3 3C8Z 5CA 0.000008299 0.54731 2.657
4 4MGD 27N 0.02333 0.40474 2.7451
5 2JHP GUN 0.04262 0.40282 2.76753
6 4RW3 SHV 0.02929 0.43334 2.98013
7 4UBS DIF 0.02632 0.41863 3.05344
8 4MAF ADX 0.02118 0.40035 3.21782
9 3IX1 NFM 0.04052 0.4069 3.64238
10 2PID YSA 0.0004383 0.41156 3.65169
11 2Z49 AMG 0.02677 0.43086 3.7037
12 4PEG 5GP 0.009375 0.45012 3.88889
13 1NC2 DOE 0.03003 0.41647 4.18605
14 2X3F APC 0.002711 0.41295 4.5614
15 2Z8G GLC GLC BGC 0.01579 0.40963 4.61255
16 3AFH GSU 0.0002426 0.49108 5.32787
17 4AG9 COA 0.02142 0.41378 5.45455
18 2HK9 SKM 0.03504 0.41057 5.45455
19 1R6U TYM 0.001093 0.43796 6.17849
20 1R6T TYM 0.0004965 0.41571 6.49895
21 2PS1 ORO 0.02711 0.41232 7.07965
22 1V47 ADX 0.006668 0.41713 7.44986
23 2CYB TYR 0.03878 0.40736 7.73994
24 3ZIU LSS 0.00001117 0.45429 8.30258
25 3GUZ PAF 0.04665 0.40064 9.09091
26 1K4M NAD 0.004665 0.40624 10.7981
27 5TVA AMP 0.03366 0.40016 10.8333
28 2V0C LEU LMS 0.000005637 0.53814 13.4686
29 4A91 GLU 0.003182 0.45592 15.7718
30 4J75 TYM 0.0001229 0.46597 18.0929
31 2QTR NXX 0.001348 0.40773 19.0476
32 1JZS MRC 0.000001755 0.58405 20.8487
33 5ABU GTG 0.03614 0.41247 21.4286
34 1M2Z BOG 0.013 0.43223 23.8095
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