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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: 84
This union binding pocket(no: 1) in the query (biounit: 5v49.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1IID NHM 1.4218
2 5DK4 5BX 1.51976
3 5DK4 ATP 1.51976
4 3ABA FLI 1.73697
5 5VLQ ANP 2.02952
6 3VSV XYS 2.58303
7 3C8Z 5CA 2.657
8 4I8P NAD 2.69231
9 3EWR APR 2.97619
10 5GUE GGS 3.02115
11 5JBX MLI 3.06513
12 1I1N SAH 3.09735
13 4LY9 1YY 3.13653
14 4LRL TTP 3.13653
15 6B2M COA 3.14685
16 5XJD 87L 3.18182
17 4PTN PYR 3.207
18 4KWD JF2 3.50318
19 3FWN ATR 3.54167
20 3FWN 6PG 3.54167
21 3LU1 UD2 3.57143
22 1RV0 NDG 3.75
23 4OAR 2S0 3.87597
24 4ONQ SFG 3.92157
25 5IXK 6EW 3.94737
26 4JWJ SAH 3.9604
27 1ME8 RVP 3.97614
28 4R57 ACO 3.97727
29 1GZ4 ATP 4.05904
30 2OYS FMN 4.05904
31 5FAG PPI 4.14634
32 3A4T SFG 4.37956
33 5ECP JAA 4.4843
34 5ECP MET 4.4843
35 3IPQ 965 4.59364
36 1BZY IMU 4.60829
37 4MFL MFK 4.63768
38 1N46 PFA 4.65116
39 2CHT TSA 4.72441
40 6FK3 PPI 5.71956
41 1SAY PYR 5.81717
42 2RHO GSP 5.84615
43 2CYC TYR 5.86667
44 5WS9 AMP 5.89474
45 5UWA 8ND 5.91133
46 1JG3 ADN 5.95745
47 3GKJ HC3 6.03448
48 4NJH SAM 6.08696
49 4NJH 2K8 6.08696
50 5D63 FUC GLA GLA 6.14334
51 1SQL GUN 6.16438
52 2C29 DQH 6.23145
53 5H5F SAM 6.41026
54 5L92 C0R 6.58537
55 5L92 MLA 6.58537
56 5XNC MTA 7.01107
57 2PS1 PRP 7.07965
58 2PS1 ORO 7.07965
59 1W5F G2P 7.08215
60 4OIV XX9 7.52212
61 2CYB TYR 7.73994
62 5YW5 ADE 7.82123
63 1HBK MYR 7.86517
64 5N5U AMP 7.96178
65 3FUU ADN 8.11808
66 3ZIU LSS 8.30258
67 1EXF GLY 9.09091
68 5L7G 6QE 9.18033
69 2A8Y MTA 9.25926
70 1MGP PLM 9.26518
71 3KFC 61X 9.48617
72 5EXE 5SR 9.55414
73 3COW 52H 9.63455
74 5B4B LP5 10.8871
75 3ZLR X0B 12.0253
76 2V0C LEU LMS 13.4686
77 2DX7 CIT 13.5965
78 1ZGA HMK 14.2857
79 3KPB SAM 15.5738
80 4A91 GLU 15.7718
81 3O5N BR0 16.0714
82 1OFU GDP 16.875
83 1JZS MRC 20.8487
84 1M2Z DEX 23.8095
Pocket No.: 2; Query (leader) PDB : 5V49; Ligand: 8WA; Similar sites found with APoc: 78
This union binding pocket(no: 2) in the query (biounit: 5v49.bio2) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZDK ATP 1.10701
2 5Y0T TAT 1.17647
3 4UCI ADN 1.20482
4 1PIG GLC GLC 1.41129
5 5WXU FLC 1.46138
6 5HV7 RBL 1.83486
7 5VLQ ANP 2.02952
8 3E5P PPI 2.15633
9 5Y0N ATP 2.29885
10 5OSW AE4 2.39852
11 5Y0Q APC 2.53456
12 3VSV XYS 2.58303
13 3C8Z 5CA 2.657
14 5HYR EST 2.71318
15 4MGD 27N 2.7451
16 2JHP GUN 2.76753
17 3DOO SKM 2.88809
18 4RW3 SHV 2.98013
19 4UBS DIF 3.05344
20 5JBX MLI 3.06513
21 5XJD 87L 3.18182
22 4MAF ADX 3.21782
23 2R4V GSH 3.23887
24 6FLZ MMA 3.47222
25 4MGA 27L 3.52941
26 4TV1 36M 3.58566
27 3IX1 NFM 3.64238
28 2PID YSA 3.65169
29 2Z49 AMG 3.7037
30 2Z48 A2G 3.7037
31 1RV0 NDG 3.75
32 1ZGS XMM 3.80313
33 4PEG 5GP 3.88889
34 2GPT SKM 4.0153
35 5FAG PPI 4.14634
36 1NC2 DOE 4.18605
37 1VJE MSE 4.21687
38 1J09 GLU 4.2735
39 1J09 ATP 4.2735
40 2X3F APC 4.5614
41 2Z8G GLC GLC BGC 4.61255
42 3LM9 ADP 4.63576
43 1A8U BEZ 4.69314
44 4OKS 2T9 5.17241
45 3AFH GSU 5.32787
46 4AG9 COA 5.45455
47 2HK9 SKM 5.45455
48 1VLH PNS 5.78035
49 1SQL GUN 6.16438
50 1R6U TYM 6.17849
51 5LX9 OLB 6.18893
52 2HHP FLC 6.41509
53 1R6T TYM 6.49895
54 3R9C ECL 6.69856
55 5X3D 7XL 6.875
56 2PS1 ORO 7.07965
57 1V47 ADX 7.44986
58 2CYB TYR 7.73994
59 5YW5 ADE 7.82123
60 5N5U AMP 7.96178
61 3ZIU LSS 8.30258
62 5HWV MBN 8.46154
63 1EXF GLY 9.09091
64 3GUZ PAF 9.09091
65 1T0S BML 9.30233
66 3COW 52H 9.63455
67 4Y4V DAL 10.6195
68 1APZ ASP 10.6383
69 1K4M NAD 10.7981
70 5TVA AMP 10.8333
71 2V0C LEU LMS 13.4686
72 5ZQ4 AMP 14.1026
73 4A91 GLU 15.7718
74 4J75 TYM 18.0929
75 2QTR NXX 19.0476
76 1JZS MRC 20.8487
77 5ABU GTG 21.4286
78 1M2Z BOG 23.8095
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