Receptor
PDB id Resolution Class Description Source Keywords
1PFV 1.7 Å EC: 6.1.1.10 METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH DIFLUOROMETHIONINE 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
2FM A:553;
 Valid;
 none;
 submit data
185.192 C5 H9 F2 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: 2FM; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 2FM 1 1
2 MED 0.514286 0.666667
3 MET 0.514286 0.666667
4 MF3 0.5 0.964286
5 API 0.454545 0.625
6 DAB 0.424242 0.65625
7 HSE 0.424242 0.636364
8 ABA 0.419355 0.62069
9 DBB 0.419355 0.62069
10 ORN 0.416667 0.677419
11 NVA 0.411765 0.666667
12 HCS 0.411765 0.758621
13 NLE 0.405405 0.625
Similar Ligands (3D)
Ligand no: 1; Ligand: 2FM; Similar ligands found: 204
No: Ligand Similarity coefficient
1 UN1 0.9889
2 OOG 0.9702
3 LYS 0.9560
4 MLZ 0.9484
5 CCU 0.9461
6 ARG 0.9456
7 TEG 0.9419
8 4TB 0.9402
9 LYN 0.9379
10 GLU 0.9372
11 0L1 0.9367
12 SLZ 0.9357
13 NNH 0.9336
14 8SZ 0.9332
15 AKG 0.9312
16 DHH 0.9292
17 PBA 0.9291
18 PHE 0.9289
19 AT3 0.9278
20 CXP 0.9274
21 NPI 0.9270
22 GLN 0.9268
23 ONH 0.9261
24 CLT 0.9256
25 2JJ 0.9248
26 GRQ 0.9223
27 6XA 0.9213
28 S8V 0.9211
29 5OY 0.9210
30 4TP 0.9209
31 9ON 0.9206
32 6HN 0.9200
33 DAR 0.9189
34 CIR 0.9187
35 GGB 0.9185
36 9YT 0.9184
37 O45 0.9182
38 4ZD 0.9180
39 TIH 0.9179
40 KNA 0.9179
41 MLY 0.9179
42 DLY 0.9171
43 1PS 0.9170
44 TCA 0.9169
45 F98 0.9166
46 HFA 0.9161
47 ILO 0.9161
48 NFA 0.9145
49 NMH 0.9144
50 IAR 0.9130
51 LUQ 0.9129
52 64Z 0.9123
53 HCI 0.9122
54 DXP 0.9114
55 TYR 0.9107
56 DPN 0.9107
57 ENV 0.9106
58 XIZ 0.9106
59 S2G 0.9105
60 7BC 0.9105
61 AG2 0.9098
62 TZP 0.9092
63 DIR 0.9088
64 KDG 0.9088
65 MSL 0.9084
66 E4P 0.9084
67 AHN 0.9080
68 P81 0.9065
69 PBN 0.9061
70 11C 0.9059
71 SHV 0.9058
72 N6C 0.9056
73 XRX 0.9054
74 KQY 0.9053
75 KPC 0.9052
76 7OD 0.9050
77 HPN 0.9044
78 9GB 0.9030
79 MHN 0.9027
80 E8U 0.9026
81 HL4 0.9023
82 M3L 0.9021
83 PML 0.9018
84 EXY 0.9015
85 ONL 0.9012
86 OSE 0.9007
87 650 0.9003
88 XOG 0.9002
89 3OM 0.9000
90 3OL 0.9000
91 1HS 0.8998
92 DTY 0.8993
93 3YP 0.8986
94 M1T 0.8983
95 HGA 0.8982
96 LPB 0.8978
97 PC 0.8977
98 Q9Z 0.8977
99 GVA 0.8975
100 58X 0.8975
101 GLR 0.8973
102 DHM 0.8968
103 2IT 0.8965
104 SME 0.8962
105 DEZ 0.8958
106 ENW 0.8954
107 5XA 0.8947
108 DXG 0.8944
109 DZA 0.8939
110 MES 0.8939
111 NWH 0.8939
112 MHO 0.8933
113 3H2 0.8929
114 IP8 0.8925
115 MSE 0.8925
116 4LW 0.8919
117 OCA 0.8917
118 7C3 0.8912
119 AHL 0.8908
120 FK8 0.8906
121 LPA 0.8902
122 1X4 0.8890
123 2NP 0.8879
124 DER 0.8876
125 IVL 0.8875
126 F06 0.8871
127 ZZU 0.8868
128 SPD 0.8866
129 QFJ 0.8865
130 LX1 0.8862
131 5SP 0.8862
132 DLT 0.8861
133 I38 0.8857
134 GGL 0.8857
135 CCD 0.8853
136 26P 0.8846
137 FOM 0.8843
138 4LR 0.8841
139 6CL 0.8838
140 SB7 0.8836
141 HF2 0.8835
142 KMT 0.8834
143 TYC 0.8834
144 JX7 0.8834
145 0A9 0.8832
146 BHU 0.8832
147 FXY 0.8831
148 CHH 0.8827
149 CS2 0.8826
150 CUW 0.8813
151 HAR 0.8811
152 Z70 0.8809
153 4LV 0.8808
154 NTU 0.8808
155 7UC 0.8807
156 0VT 0.8806
157 PRO GLY 0.8790
158 Q06 0.8789
159 KPA 0.8776
160 ABF 0.8767
161 ACA 0.8757
162 PFF 0.8754
163 RTK 0.8753
164 XRS 0.8749
165 MEQ 0.8747
166 7XA 0.8746
167 EOU 0.8745
168 NSD 0.8744
169 011 0.8740
170 DX5 0.8737
171 EN1 0.8734
172 TB8 0.8732
173 4JK 0.8729
174 WT2 0.8729
175 PJL 0.8715
176 EGV 0.8711
177 3GZ 0.8706
178 NMM 0.8705
179 AE3 0.8702
180 R5P 0.8701
181 R52 0.8701
182 OC9 0.8695
183 OCT 0.8694
184 PG0 0.8682
185 B3U 0.8680
186 5RP 0.8676
187 5LD 0.8672
188 4BF 0.8667
189 SSC 0.8661
190 OYA 0.8656
191 NM3 0.8651
192 RA7 0.8649
193 16D 0.8644
194 9J6 0.8643
195 5DL 0.8640
196 LGT 0.8637
197 BL0 0.8632
198 FB6 0.8631
199 PCS 0.8626
200 HIC 0.8595
201 DA3 0.8578
202 SG3 0.8538
203 OHJ 0.8537
204 37E 0.8513
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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