Receptor
PDB id Resolution Class Description Source Keywords
1PFW 1.78 Å EC: 6.1.1.10 METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH TRIFLUOROMETHIONINE 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MF3 A:553;
 Valid;
 none;
 submit data
203.183 C5 H8 F3 N O2 S C(CSC...
ZN A:552;
 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: MF3; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 MF3 1 1
2 MET 0.5 0.647059
3 2FM 0.5 0.964286
4 MED 0.5 0.647059
5 DGL 0.416667 0.625
6 GGL 0.416667 0.625
7 GLU 0.416667 0.625
8 DAB 0.411765 0.636364
9 HSE 0.411765 0.617647
10 ABA 0.40625 0.6
11 DBB 0.40625 0.6
12 API 0.4 0.606061
13 HCS 0.4 0.733333
14 NVA 0.4 0.645161
Similar Ligands (3D)
Ligand no: 1; Ligand: MF3; Similar ligands found: 246
No: Ligand Similarity coefficient
1 UN1 0.9645
2 F98 0.9603
3 2JJ 0.9513
4 5OY 0.9510
5 OOG 0.9468
6 KPC 0.9405
7 1PS 0.9395
8 DXP 0.9375
9 LUQ 0.9337
10 4TP 0.9330
11 QFJ 0.9326
12 FOM 0.9304
13 ARG 0.9298
14 TZP 0.9294
15 9GB 0.9246
16 1HS 0.9237
17 Q04 0.9232
18 MES 0.9224
19 PC 0.9210
20 PPY 0.9201
21 SHI 0.9200
22 4TB 0.9195
23 0L1 0.9195
24 6HN 0.9189
25 3PG 0.9185
26 LYS 0.9182
27 DER 0.9170
28 P81 0.9170
29 HFA 0.9159
30 TIH 0.9155
31 CIR 0.9153
32 9YT 0.9148
33 NPI 0.9138
34 LX1 0.9135
35 GGB 0.9134
36 MLZ 0.9128
37 XRX 0.9128
38 DHH 0.9127
39 HCI 0.9115
40 DEZ 0.9104
41 5SP 0.9103
42 TX4 0.9103
43 PHE 0.9101
44 ILO 0.9099
45 11C 0.9091
46 A5P 0.9088
47 TEG 0.9084
48 NNH 0.9083
49 DHC 0.9078
50 DX5 0.9076
51 KPA 0.9075
52 IVL 0.9068
53 DAR 0.9060
54 4ZD 0.9059
55 GLR 0.9052
56 BCH 0.9048
57 DHM 0.9040
58 E4P 0.9037
59 DXG 0.9037
60 1X4 0.9034
61 KDG 0.9034
62 M3L 0.9029
63 3S5 0.9028
64 TYR 0.9027
65 IAR 0.9021
66 CCD 0.9020
67 MLY 0.9019
68 CXP 0.9017
69 DZA 0.9014
70 S8V 0.9011
71 XOG 0.9010
72 PML 0.9009
73 NSB 0.9006
74 AT3 0.9005
75 ENO 0.8997
76 58X 0.8993
77 NFA 0.8990
78 TCA 0.8983
79 MSL 0.8983
80 KNA 0.8976
81 2NP 0.8972
82 HC4 0.8970
83 7OD 0.8966
84 PBA 0.8966
85 AHC 0.8964
86 DLY 0.8964
87 AHN 0.8958
88 ENW 0.8956
89 GVA 0.8956
90 5RP 0.8955
91 EGV 0.8948
92 HSX 0.8948
93 PPT 0.8947
94 5LD 0.8947
95 GRQ 0.8946
96 C82 0.8939
97 6CL 0.8936
98 Z70 0.8924
99 3YP 0.8924
100 GPJ 0.8923
101 LYN 0.8921
102 BL0 0.8920
103 HPV 0.8920
104 E8U 0.8919
105 PBN 0.8915
106 FK8 0.8915
107 XIZ 0.8914
108 7BC 0.8913
109 PRO GLY 0.8912
110 B3U 0.8910
111 AHL 0.8908
112 8SZ 0.8905
113 HGA 0.8903
114 5DL 0.8902
115 Q06 0.8901
116 650 0.8900
117 SB7 0.8900
118 ONH 0.8900
119 DIR 0.8898
120 1L5 0.8891
121 HPP 0.8890
122 DTY 0.8888
123 ENV 0.8888
124 EN1 0.8887
125 IP8 0.8885
126 EXY 0.8884
127 D5X 0.8879
128 PO6 0.8878
129 26P 0.8874
130 64Z 0.8872
131 CHH 0.8872
132 XRS 0.8870
133 PFF 0.8870
134 OCA 0.8870
135 DLT 0.8869
136 O45 0.8869
137 SLZ 0.8853
138 ABH 0.8844
139 N9J 0.8841
140 4LW 0.8833
141 S0W 0.8833
142 JX7 0.8828
143 R5P 0.8826
144 2FX 0.8822
145 DAH 0.8816
146 RP5 0.8816
147 ZZU 0.8815
148 MHN 0.8803
149 RTK 0.8802
150 ABF 0.8802
151 GPF 0.8800
152 KQY 0.8799
153 GLY GLY GLY 0.8795
154 GUA 0.8787
155 HXY 0.8784
156 HAR 0.8778
157 HPN 0.8775
158 4LR 0.8774
159 RES 0.8770
160 HRG 0.8766
161 6C5 0.8762
162 4LV 0.8760
163 PJL 0.8759
164 XI7 0.8758
165 PMV 0.8756
166 NM3 0.8754
167 LPB 0.8751
168 MHO 0.8751
169 ATX 0.8748
170 SOJ 0.8742
171 EOU 0.8740
172 2HC 0.8740
173 N6C 0.8739
174 RP3 0.8738
175 PCS 0.8734
176 SG3 0.8732
177 EYV 0.8732
178 0A9 0.8732
179 MEQ 0.8731
180 HMS 0.8731
181 SHV 0.8731
182 AG2 0.8730
183 4BF 0.8729
184 FXY 0.8727
185 HIC 0.8726
186 TYC 0.8720
187 HF2 0.8718
188 6C9 0.8714
189 F06 0.8714
190 GB5 0.8713
191 LPA 0.8712
192 HL4 0.8711
193 RKV 0.8710
194 5TO 0.8710
195 1AE 0.8709
196 WT2 0.8709
197 YOF 0.8707
198 9J6 0.8701
199 F90 0.8700
200 MP5 0.8700
201 4FE 0.8694
202 TB8 0.8693
203 ACA 0.8689
204 R52 0.8686
205 FB6 0.8680
206 4JK 0.8678
207 TOH 0.8677
208 NMH 0.8674
209 KYN 0.8670
210 5WN 0.8667
211 LGT 0.8667
212 SME 0.8664
213 GAE 0.8658
214 7C3 0.8655
215 CUW 0.8653
216 6ZX 0.8652
217 3H2 0.8651
218 NMM 0.8649
219 37E 0.8648
220 P7Y 0.8648
221 4FP 0.8648
222 11X 0.8637
223 0A1 0.8628
224 A51 0.8627
225 RGP 0.8623
226 R10 0.8622
227 P4F 0.8606
228 P93 0.8600
229 EQW 0.8596
230 7O4 0.8595
231 5OO 0.8594
232 MMS 0.8594
233 QH3 0.8594
234 URP 0.8593
235 657 0.8587
236 SSC 0.8573
237 STX 0.8572
238 HBU 0.8567
239 KPV 0.8557
240 5XA 0.8556
241 6FG 0.8554
242 EUH 0.8548
243 9J3 0.8537
244 0NX 0.8534
245 ALY 0.8512
246 M45 0.8512
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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