Receptor
PDB id Resolution Class Description Source Keywords
3AFH 2 Å EC: 6.1.1.17 CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA NONDISCRIMINATING G TRNA SYNTHETASE IN COMPLEX WITH A GLUTAMYL-AMP ANALOG THERMOTOGA MARITIMA PROTEIN-SUBSTRATE COMPLEX NON-DISCRIMINATING GLUTAMYL-TRNA SYNTHETASE AMINOACYL-TRNA SYNTHETASE ATP-BINDING LIGASENUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS
Ref.: STRUCTURE OF NONDISCRIMINATING GLUTAMYL-TRNA SYNTHE THERMOTOGA MARITIMA ACTA CRYSTALLOGR.,SECT.D V. 66 813 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GSU A:2001;
Valid;
none;
submit data
475.434 C15 H21 N7 O9 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3AFH 2 Å EC: 6.1.1.17 CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA NONDISCRIMINATING G TRNA SYNTHETASE IN COMPLEX WITH A GLUTAMYL-AMP ANALOG THERMOTOGA MARITIMA PROTEIN-SUBSTRATE COMPLEX NON-DISCRIMINATING GLUTAMYL-TRNA SYNTHETASE AMINOACYL-TRNA SYNTHETASE ATP-BINDING LIGASENUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS
Ref.: STRUCTURE OF NONDISCRIMINATING GLUTAMYL-TRNA SYNTHE THERMOTOGA MARITIMA ACTA CRYSTALLOGR.,SECT.D V. 66 813 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3AFH - GSU C15 H21 N7 O9 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3AFH - GSU C15 H21 N7 O9 S c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3AFH - GSU C15 H21 N7 O9 S c1nc(c2c(n....
2 2CUZ - GLU C5 H9 N O4 C(CC(=O)O)....
3 1N75 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1J09 - GLU C5 H9 N O4 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GSU; Similar ligands found: 214
No: Ligand ECFP6 Tc MDL keys Tc
1 GSU 1 1
2 DSZ 0.808989 0.97619
3 SSA 0.804598 0.952941
4 KAA 0.802198 0.942529
5 5CA 0.786517 0.952941
6 LSS 0.769231 0.931035
7 A5A 0.752809 0.940476
8 54H 0.736264 0.918605
9 VMS 0.736264 0.918605
10 TSB 0.728261 0.929412
11 53H 0.728261 0.908046
12 YSA 0.72449 0.952941
13 NVA LMS 0.723404 0.931035
14 52H 0.717391 0.908046
15 LEU LMS 0.697917 0.909091
16 NSS 0.694737 0.952941
17 G5A 0.681319 0.952941
18 WSA 0.654206 0.964286
19 5AS 0.633333 0.886364
20 P5A 0.607843 0.931818
21 4YB 0.587156 0.976471
22 649 0.566372 0.931818
23 SON 0.557895 0.813953
24 XAH 0.550459 0.8
25 5X8 0.546392 0.75
26 AHX 0.542857 0.806818
27 CA0 0.536082 0.802326
28 5AL 0.534653 0.811765
29 AMO 0.533333 0.835294
30 SLU 0.532787 0.897727
31 AMP 0.532609 0.776471
32 A 0.532609 0.776471
33 SAH 0.53 0.752941
34 SRP 0.524272 0.835294
35 7MD 0.522124 0.820225
36 AMP MG 0.521277 0.738636
37 AOC 0.521277 0.697674
38 ADX 0.520408 0.894118
39 SA8 0.52 0.7
40 WAQ 0.518519 0.816092
41 A2D 0.515789 0.77907
42 ABM 0.515789 0.758621
43 SFG 0.515152 0.738095
44 SRA 0.510638 0.802326
45 AN2 0.510204 0.790698
46 A12 0.505155 0.772727
47 BA3 0.505155 0.77907
48 AP2 0.505155 0.772727
49 AU1 0.50505 0.781609
50 LAD 0.504587 0.818182
51 SAI 0.5 0.724138
52 B4P 0.5 0.77907
53 ADP 0.5 0.77907
54 XYA 0.5 0.694118
55 5CD 0.5 0.682353
56 DAL AMP 0.5 0.790698
57 RAB 0.5 0.694118
58 AP5 0.5 0.77907
59 NB8 0.5 0.827586
60 ME8 0.5 0.820225
61 ADN 0.5 0.694118
62 TXA 0.5 0.793103
63 8QN 0.495327 0.811765
64 S7M 0.495238 0.722222
65 GAP 0.495146 0.781609
66 3DH 0.494624 0.678161
67 EEM 0.490385 0.684783
68 M33 0.49 0.770115
69 ADP MG 0.49 0.75
70 5N5 0.488636 0.674419
71 YAP 0.486726 0.825581
72 50T 0.485149 0.75
73 ACP 0.485149 0.781609
74 BEF ADP 0.485149 0.733333
75 ATP 0.485149 0.77907
76 ADP BEF 0.485149 0.733333
77 A4D 0.483146 0.694118
78 SMM 0.481132 0.717391
79 SAM 0.480769 0.722222
80 ANP 0.480769 0.781609
81 APR 0.480392 0.8
82 PRX 0.480392 0.761364
83 AQP 0.480392 0.77907
84 AR6 0.480392 0.8
85 5FA 0.480392 0.77907
86 APC 0.480392 0.772727
87 DTA 0.478261 0.709302
88 PAJ 0.477064 0.758242
89 A1R 0.477064 0.775281
90 0UM 0.477064 0.692308
91 4AD 0.477064 0.825581
92 AGS 0.475728 0.804598
93 SAP 0.475728 0.804598
94 RBY 0.475728 0.793103
95 ADV 0.475728 0.793103
96 ADP PO3 0.475728 0.776471
97 AD9 0.475728 0.761364
98 ARG AMP 0.474576 0.771739
99 FA5 0.473684 0.835294
100 DLL 0.472727 0.811765
101 ADP ALF 0.471698 0.725275
102 ALF ADP 0.471698 0.725275
103 ATP MG 0.471154 0.75
104 7MC 0.471074 0.802198
105 YLB 0.471074 0.782609
106 YLP 0.470588 0.782609
107 TYR AMP 0.469565 0.793103
108 KB1 0.469027 0.692308
109 K15 0.468468 0.677419
110 3UK 0.468468 0.802326
111 OOB 0.46789 0.811765
112 EP4 0.467391 0.644444
113 ANP MG 0.46729 0.764045
114 ACQ 0.466667 0.781609
115 TAT 0.466667 0.793103
116 A3S 0.465347 0.729412
117 A7D 0.465347 0.72093
118 9SN 0.464912 0.766667
119 PR8 0.464286 0.808989
120 6RE 0.463918 0.688889
121 M2T 0.462366 0.666667
122 SXZ 0.460177 0.722222
123 FYA 0.460177 0.790698
124 1ZZ 0.460177 0.76087
125 PTJ 0.460177 0.766667
126 62X 0.459459 0.663158
127 00A 0.459459 0.775281
128 YLC 0.459016 0.8
129 A22 0.458716 0.770115
130 MAP 0.458716 0.764045
131 48N 0.458333 0.786517
132 ATF 0.457944 0.752809
133 MTA 0.457447 0.678161
134 VRT 0.457143 0.715909
135 MYR AMP 0.45614 0.741935
136 ADP BMA 0.455357 0.761364
137 OAD 0.455357 0.802326
138 25A 0.454545 0.77907
139 A3N 0.454545 0.651685
140 J7C 0.454545 0.696629
141 VO4 ADP 0.453704 0.770115
142 ADP VO4 0.453704 0.770115
143 ZAS 0.453608 0.693182
144 AMP DBH 0.452991 0.741573
145 IOT 0.451613 0.774194
146 TYM 0.45082 0.835294
147 ADQ 0.45045 0.781609
148 GJV 0.45 0.681319
149 7C5 0.449153 0.719101
150 YLA 0.448 0.782609
151 3OD 0.447368 0.802326
152 DSH 0.444444 0.696629
153 AYB 0.444444 0.774194
154 NXX 0.442623 0.793103
155 DND 0.442623 0.793103
156 A3T 0.442308 0.697674
157 TAD 0.441667 0.777778
158 S8M 0.441441 0.747126
159 5SV 0.441441 0.728261
160 ALF ADP 3PG 0.439024 0.758242
161 LA8 ALF 3PG 0.439024 0.758242
162 LAQ 0.438017 0.8
163 COD 0.4375 0.757895
164 S4M 0.435644 0.663158
165 BIS 0.434783 0.755556
166 JB6 0.434783 0.816092
167 LPA AMP 0.434426 0.78022
168 D3Y 0.432432 0.712644
169 YLY 0.431818 0.774194
170 MAO 0.431373 0.728261
171 25L 0.431034 0.770115
172 A3G 0.43 0.72093
173 NEC 0.43 0.636364
174 KH3 0.429752 0.670213
175 GEK 0.428571 0.767442
176 4UV 0.428571 0.784091
177 OMR 0.427419 0.752688
178 TXE 0.427419 0.755556
179 5AD 0.426966 0.630952
180 3NZ 0.426087 0.707865
181 A A 0.426087 0.758621
182 AAT 0.422018 0.681319
183 4UU 0.421488 0.784091
184 NAX 0.419355 0.788889
185 6V0 0.419355 0.747253
186 TXD 0.419355 0.755556
187 NAI 0.419355 0.755556
188 MHZ 0.419048 0.673684
189 NAD IBO 0.418605 0.744444
190 SO8 0.416667 0.674157
191 AF3 ADP 3PG 0.416 0.758242
192 2VA 0.415094 0.681818
193 AHZ 0.414634 0.76087
194 3AM 0.414141 0.744186
195 ATP A A A 0.411765 0.767442
196 N0B 0.411765 0.782609
197 AFH 0.409836 0.758242
198 AR6 AR6 0.409836 0.77907
199 Y3J 0.408602 0.616279
200 7D5 0.408163 0.707865
201 4UW 0.408 0.758242
202 A5D 0.407407 0.709302
203 7D7 0.406593 0.632184
204 GTA 0.406504 0.723404
205 2SA 0.405405 0.813953
206 NAD 0.40458 0.790698
207 A3P 0.403846 0.776471
208 A2P 0.403846 0.764706
209 T5A 0.403101 0.744681
210 594 0.402985 0.852632
211 G3A 0.401639 0.747253
212 BT5 0.401515 0.793478
213 BS5 0.4 0.819149
214 CNA 0.4 0.793103
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3AFH; Ligand: GSU; Similar sites found: 55
This union binding pocket(no: 1) in the query (biounit: 3afh.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GDN FAD 0.02563 0.40594 1.02459
2 2GKS ADP 0.001448 0.41389 1.22951
3 4Z24 FAD 0.0135 0.41859 1.43443
4 1GPE FAD 0.01053 0.42642 1.63934
5 2NZ5 226 0.01238 0.4 1.69492
6 4MAF ADX 0.0001225 0.47827 1.73267
7 1KQN NAD 0.01503 0.40622 1.79211
8 4GID 0GH 0.03149 0.42632 1.80412
9 3KFL ME8 0.000001206 0.5023 1.84426
10 1PFY MSP 0.000002023 0.49891 2.04918
11 4YNU FAD 0.03092 0.40278 2.04918
12 3MBC NAP 0.02107 0.40046 2.04918
13 4M0R 644 0.02721 0.40383 2.11082
14 3C8Z 5CA 0.00000008122 0.58871 2.41546
15 3ZIU LSS 0.000002711 0.56372 2.45902
16 1UH4 GLC GLC GLC GLC GLC GLC 0.0188 0.41607 2.45902
17 1R6T TYM 0.00002749 0.40309 2.51572
18 4YHB FAD 0.01177 0.4034 2.5641
19 2QTR NXX 0.0001119 0.40074 2.6455
20 5HSA FAS 0.009263 0.42555 2.66393
21 4C2C ALA ALA ALA 0.005042 0.42933 2.69058
22 1N4W FAD 0.02644 0.40528 2.86885
23 5A5W GUO 0.0165 0.41163 3.16206
24 1K4M NAD 0.00007614 0.43648 3.28639
25 1TDF FAD 0.02095 0.41267 4.11392
26 3QX9 ATP 0.005102 0.437 4.34783
27 1JZS MRC 0.0001131 0.47299 4.5082
28 2X3F APC 0.000003866 0.46709 4.5614
29 1OBD AMP 0.006004 0.41932 4.57516
30 5FJN BE2 0.02509 0.40803 4.60526
31 5FJN FAD 0.0223 0.40803 4.60526
32 1O6B ADP 0.00932 0.41583 5.32544
33 5V49 8WA 0.0002426 0.49108 5.32787
34 4C3Y ANB 0.02152 0.4121 5.32787
35 4C3Y FAD 0.01762 0.4121 5.32787
36 1R6U TYM 0.00003557 0.51566 5.49199
37 5LLT DND 0.0002664 0.48625 6.10329
38 1JIL 485 0.001882 0.41408 6.42857
39 1V47 ADX 0.0002413 0.47007 6.59026
40 4G0P U5P 0.01152 0.41537 6.80272
41 1RZM E4P 0.01711 0.40932 6.80473
42 4NAT 2W5 0.01836 0.40746 6.875
43 4UP3 FAD 0.008985 0.42523 7.00637
44 1N1D C2G 0.0003591 0.40289 7.75194
45 1YUM NCN 0.00104 0.44406 7.85124
46 4U60 SIA GAL NGA 0.02844 0.40088 7.85714
47 2X1L ADN 0.00002497 0.5208 8.60656
48 2V0C LEU LMS 0.000001343 0.5774 8.81148
49 1WQ1 AF3 0.008117 0.4297 9.63855
50 4N14 WR7 0.02797 0.41063 10.1911
51 4J75 TYM 0.000001177 0.58915 10.2689
52 2PID YSA 0.00001656 0.45436 10.3933
53 3EXS 5RP 0.01541 0.40091 17.1946
54 3ND6 ATP 0.01481 0.40652 26.3158
55 4A91 GLU 0.00000000437 0.79903 46.3087
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