Receptor
PDB id Resolution Class Description Source Keywords
6SPN 1.45 Å EC: 6.1.1.10 STRUCTURE OF THE ESCHERICHIA COLI METHIONYL-TRNA SYNTHETASE WITH BETA-METHIONINE ESCHERICHIA COLI TRNA AMINOACYLATION TRANSLATION
Ref.: USE OF BETA3-METHIONINE AS AN AMINO ACID SUBSTRATE ESCHERICHIA COLI METHIONYL-TRNA SYNTHETASE. J.STRUCT.BIOL. V. 209 07435 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B3M A:604;
A:603;
 Valid;
Valid;
 none;
Atoms found MORE than expected: % Diff = 2;
 Kd = 1.2 mM
163.238 C6 H13 N O2 S CSCC[...
GOL A:605;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
ZN A:601;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
CIT A:602;
 Invalid;
 none;
 submit data
192.124 C6 H8 O7 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1PFY 1.93 Å EC: 6.1.1.10 METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONYL SULPHAMOYL ADENOSINE ESCHERICHIA COLI ROSSMANN FOLD LIGASE
Ref.: USE OF ANALOGUES OF METHIONINE AND METHIONYL ADENYLATE TO SAMPLE CONFORMATIONAL CHANGES DURING CATALYSIS IN ESCHERICHIA COLI METHIONYL-TRNA SYNTHETASE. J.MOL.BIOL. V. 332 59 2003
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1PFV - 2FM C5 H9 F2 N O2 S C(CSC(F)F)....
2 1PG2 - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6SPR Kd = 0.56 mM B3M C6 H13 N O2 S CSCC[C@@H]....
4 1PFU Kd = 1900 uM MPJ C4 H12 N O2 P S CSCC[C@H](....
5 1F4L - MET C5 H11 N O2 S CSCC[C@@H]....
6 3H9B - NOT C6 H12 N4 O2 C(CCN=[N+]....
7 1PFW - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
8 1PG0 Kd ~ 1 uM MOD C15 H27 N6 O7 P S CSCC[C@@H]....
9 6SPO Kd = 0.05 mM MET C5 H11 N O2 S CSCC[C@@H]....
10 1PFY ic50 ~ 7 nM MSP C15 H25 N7 O7 S2 CSCC[C@@H]....
11 3H99 - MET C5 H11 N O2 S CSCC[C@@H]....
12 1P7P - MPH C4 H12 N O3 P S CSCC[C@H](....
13 6SPN Kd = 1.2 mM B3M C6 H13 N O2 S CSCC[C@@H]....
14 6SPQ Kd = 0.029 mM MET C5 H11 N O2 S CSCC[C@@H]....
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 1PFV - 2FM C5 H9 F2 N O2 S C(CSC(F)F)....
2 1PG2 - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6SPR Kd = 0.56 mM B3M C6 H13 N O2 S CSCC[C@@H]....
4 1PFU Kd = 1900 uM MPJ C4 H12 N O2 P S CSCC[C@H](....
5 1F4L - MET C5 H11 N O2 S CSCC[C@@H]....
6 3H9B - NOT C6 H12 N4 O2 C(CCN=[N+]....
7 1PFW - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
8 1PG0 Kd ~ 1 uM MOD C15 H27 N6 O7 P S CSCC[C@@H]....
9 6SPO Kd = 0.05 mM MET C5 H11 N O2 S CSCC[C@@H]....
10 1PFY ic50 ~ 7 nM MSP C15 H25 N7 O7 S2 CSCC[C@@H]....
11 3H99 - MET C5 H11 N O2 S CSCC[C@@H]....
12 1P7P - MPH C4 H12 N O3 P S CSCC[C@H](....
13 6SPN Kd = 1.2 mM B3M C6 H13 N O2 S CSCC[C@@H]....
14 6SPQ Kd = 0.029 mM MET C5 H11 N O2 S CSCC[C@@H]....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1PFV - 2FM C5 H9 F2 N O2 S C(CSC(F)F)....
2 1PG2 - ADN C10 H13 N5 O4 c1nc(c2c(n....
3 6SPR Kd = 0.56 mM B3M C6 H13 N O2 S CSCC[C@@H]....
4 1PFU Kd = 1900 uM MPJ C4 H12 N O2 P S CSCC[C@H](....
5 1F4L - MET C5 H11 N O2 S CSCC[C@@H]....
6 3H9B - NOT C6 H12 N4 O2 C(CCN=[N+]....
7 1PFW - MF3 C5 H8 F3 N O2 S C(CSC(F)(F....
8 1PG0 Kd ~ 1 uM MOD C15 H27 N6 O7 P S CSCC[C@@H]....
9 6SPO Kd = 0.05 mM MET C5 H11 N O2 S CSCC[C@@H]....
10 1PFY ic50 ~ 7 nM MSP C15 H25 N7 O7 S2 CSCC[C@@H]....
11 3H99 - MET C5 H11 N O2 S CSCC[C@@H]....
12 1P7P - MPH C4 H12 N O3 P S CSCC[C@H](....
13 6SPN Kd = 1.2 mM B3M C6 H13 N O2 S CSCC[C@@H]....
14 6SPQ Kd = 0.029 mM MET C5 H11 N O2 S CSCC[C@@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: B3M; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 B3M 1 1
2 MED 0.472222 0.8125
3 MET 0.472222 0.8125
Similar Ligands (3D)
Ligand no: 1; Ligand: B3M; Similar ligands found: 149
No: Ligand Similarity coefficient
1 AG2 0.9422
2 KMH 0.9405
3 SHV 0.9386
4 IXW 0.9327
5 KQY 0.9318
6 ORN 0.9257
7 ACA 0.9250
8 LYS 0.9233
9 7UC 0.9222
10 N6C 0.9209
11 HPN 0.9190
12 NLE 0.9161
13 3H2 0.9156
14 GLU 0.9147
15 AKG 0.9146
16 PBN 0.9139
17 OCA 0.9137
18 0L1 0.9136
19 1CO 0.9120
20 MEV 0.9117
21 CUW 0.9116
22 SSB 0.9112
23 2CO 0.9101
24 OCT 0.9090
25 NMH 0.9087
26 NWH 0.9058
27 RB5 0.9054
28 GVA 0.9050
29 PML 0.9040
30 KMT 0.9033
31 MSE 0.9021
32 MPH 0.9017
33 GLN 0.9016
34 3HG 0.8995
35 M1T 0.8992
36 MHO 0.8991
37 MPJ 0.8988
38 7C3 0.8980
39 AE3 0.8976
40 8EW 0.8966
41 GLY GLY 0.8960
42 DLY 0.8936
43 5XA 0.8931
44 6XA 0.8930
45 XLS 0.8929
46 PG0 0.8915
47 8SZ 0.8912
48 ONL 0.8911
49 MTL 0.8909
50 GOJ 0.8904
51 GPF 0.8903
52 6NA 0.8903
53 SLZ 0.8901
54 3YP 0.8901
55 4SD 0.8891
56 16D 0.8886
57 2EH 0.8884
58 RNS 0.8882
59 6JN 0.8882
60 NSD 0.8881
61 MHN 0.8879
62 S2G 0.8879
63 P23 0.8871
64 LLH 0.8867
65 O45 0.8867
66 2HG 0.8866
67 BHU 0.8860
68 HPO 0.8855
69 DXG 0.8854
70 MLT 0.8849
71 NLP 0.8848
72 MLZ 0.8844
73 152 0.8842
74 AHN 0.8834
75 BHL 0.8832
76 SD4 0.8808
77 7XA 0.8792
78 5XB 0.8790
79 XUL 0.8790
80 HTX 0.8790
81 OOG 0.8788
82 SME 0.8786
83 011 0.8783
84 9J3 0.8777
85 LT1 0.8771
86 DZA 0.8771
87 1N5 0.8763
88 13P 0.8761
89 GRQ 0.8758
90 ENV 0.8757
91 RBL 0.8751
92 258 0.8750
93 OHJ 0.8750
94 OC9 0.8748
95 ARG 0.8746
96 MAH 0.8740
97 VKC 0.8740
98 OYA 0.8738
99 263 0.8736
100 GPJ 0.8731
101 NYL 0.8731
102 BNF 0.8729
103 2IT 0.8727
104 DER 0.8720
105 HMS 0.8717
106 DII 0.8716
107 AEF 0.8711
108 HPL 0.8705
109 AT3 0.8705
110 DGL 0.8703
111 XYL 0.8702
112 P22 0.8698
113 3LR 0.8693
114 EKN 0.8686
115 M44 0.8685
116 SHO 0.8684
117 43W 0.8680
118 3OL 0.8679
119 UN1 0.8679
120 BHL BHL 0.8673
121 SEP 0.8673
122 B40 0.8668
123 ENW 0.8666
124 GLR 0.8665
125 NTU 0.8664
126 N4B 0.8655
127 FUD 0.8645
128 1H1 0.8633
129 URP 0.8626
130 0VT 0.8619
131 LPK 0.8615
132 HL5 0.8614
133 5FX 0.8614
134 4TB 0.8608
135 KNA 0.8601
136 S8V 0.8598
137 DIR 0.8596
138 DAR 0.8594
139 DAV 0.8582
140 PSJ 0.8572
141 ROR 0.8568
142 CLT 0.8563
143 GGL 0.8561
144 DKA 0.8556
145 E79 0.8553
146 I38 0.8530
147 EHM 0.8526
148 SKJ 0.8522
149 KDG 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1PFY; Ligand: MSP; 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: 1pfy.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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