Receptor
PDB id Resolution Class Description Source Keywords
3H9B 1.5 Å EC: 6.1.1.10 STRUCTURE OF A MUTANT METHIONYL-TRNA SYNTHETASE WITH MODIFIE SPECIFICITY COMPLEXED WITH AZIDONORLEUCINE ESCHERICHIA COLI ROSSMANN FOLD AMINOACYL-TRNA SYNTHETASE ATP-BINDING LIGASBINDING NUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS RNA-BINDTRNA-BINDING
Ref.: SWITCHING FROM AN INDUCED-FIT TO A LOCK-AND-KEY MEC AN AMINOACYL-TRNA SYNTHETASE WITH MODIFIED SPECIFIC J.MOL.BIOL. V. 394 843 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT A:603;
A:604;
 Invalid;
Invalid;
 none;
none;
 submit data
192.124 C6 H8 O7 C(C(=...
NOT A:602;
 Valid;
 none;
 submit data
172.185 C6 H12 N4 O2 C(CCN...
ZN A:601;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
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: NOT; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 NOT 1 1
2 DLY 0.475 0.735294
3 LYS 0.463415 0.764706
4 API 0.459459 0.611111
5 ORN 0.425 0.705882
6 MLZ 0.422222 0.609756
7 6HN 0.422222 0.704545
Similar Ligands (3D)
Ligand no: 1; Ligand: NOT; Similar ligands found: 135
No: Ligand Similarity coefficient
1 NPI 0.9487
2 MLY 0.9423
3 EXY 0.9416
4 OCA 0.9398
5 ARG 0.9392
6 CIR 0.9352
7 NMM 0.9340
8 DNN 0.9332
9 HPL 0.9332
10 KNA 0.9303
11 ALY 0.9297
12 4JK 0.9293
13 WT2 0.9293
14 HRG 0.9239
15 7XA 0.9233
16 HAR 0.9223
17 NNH 0.9218
18 ODI 0.9201
19 M3L 0.9183
20 XOG 0.9172
21 DHH 0.9157
22 8AC 0.9130
23 DKA 0.9113
24 CLT 0.9113
25 4DI 0.9103
26 GGB 0.9096
27 E8U 0.9087
28 IAR 0.9086
29 DAR 0.9086
30 011 0.9086
31 PML 0.9076
32 NFZ 0.9075
33 DIA 0.9071
34 TEG 0.9069
35 KAP 0.9068
36 ILO 0.9063
37 26P 0.9051
38 S2C 0.9044
39 1N5 0.9038
40 JX7 0.9037
41 ABH 0.9034
42 ZE7 0.9024
43 SB7 0.9017
44 3KJ 0.9016
45 LPA 0.9010
46 GVA 0.9008
47 HL6 0.8995
48 D10 0.8993
49 UN1 0.8982
50 GB5 0.8974
51 N8C 0.8973
52 GC7 0.8972
53 DA2 0.8972
54 DDK 0.8971
55 SPD 0.8968
56 0XR 0.8956
57 6C8 0.8955
58 ENV 0.8951
59 FXY 0.8941
60 9OD 0.8940
61 JM2 0.8928
62 37Z 0.8921
63 OYA 0.8917
64 OOG 0.8916
65 ZZU 0.8910
66 AHL 0.8900
67 FB6 0.8894
68 OC9 0.8893
69 9J6 0.8891
70 DDW 0.8875
71 64Z 0.8870
72 4KJ 0.8869
73 Z70 0.8868
74 SS9 0.8862
75 19N 0.8862
76 5PV 0.8860
77 5UF 0.8856
78 XRX 0.8855
79 3GZ 0.8842
80 ENW 0.8829
81 6FG 0.8828
82 N9M 0.8825
83 SLZ 0.8820
84 LYN 0.8810
85 LPB 0.8798
86 1OV 0.8795
87 U4G 0.8795
88 G3M 0.8795
89 5KJ 0.8790
90 2NP 0.8772
91 RGP 0.8772
92 OKS 0.8764
93 IJ6 0.8742
94 MGB 0.8741
95 ONH 0.8731
96 5TO 0.8729
97 HPN 0.8725
98 XI7 0.8720
99 DTB 0.8718
100 PUW 0.8716
101 6C5 0.8713
102 RED 0.8712
103 GOE 0.8707
104 OJM 0.8705
105 KPV 0.8705
106 KPC 0.8704
107 58X 0.8702
108 HPO 0.8699
109 GRQ 0.8697
110 P93 0.8679
111 5OY 0.8670
112 EGV 0.8664
113 6C4 0.8662
114 6C9 0.8660
115 37E 0.8658
116 11X 0.8658
117 AE3 0.8656
118 GGG 0.8653
119 YIP 0.8646
120 M1T 0.8636
121 SHV 0.8632
122 0L1 0.8631
123 OJD 0.8629
124 LUQ 0.8628
125 4TB 0.8611
126 TZP 0.8610
127 3CX 0.8609
128 KQY 0.8608
129 NWH 0.8593
130 NMH 0.8592
131 VUR 0.8581
132 4YZ 0.8564
133 FHV 0.8560
134 1HS 0.8537
135 S0B 0.8510
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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