Receptor
PDB id Resolution Class Description Source Keywords
3a5y 1.9 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF GENX FROM ESCHERICHIA COLI IN COMPLEX W LYSYLADENYLATE ANALOG ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE LYSYLADENYLATE ANALOG AMINOACYL-TRNA SYNTHETASLIGASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PRSTRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KAA A:1990;
B:1991;
C:1992;
D:1993;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 11 nM
474.492 C16 H26 N8 O7 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A5Y 1.9 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF GENX FROM ESCHERICHIA COLI IN COMPLEX W LYSYLADENYLATE ANALOG ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE LYSYLADENYLATE ANALOG AMINOACYL-TRNA SYNTHETASLIGASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PRSTRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3G1Z - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3G1Z - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: KAA; Similar ligands found: 278
No: Ligand ECFP6 Tc MDL keys Tc
1 KAA 1 1
2 SSA 0.804598 0.942529
3 GSU 0.802198 0.942529
4 5CA 0.786517 0.942529
5 DSZ 0.769231 0.920455
6 LSS 0.769231 0.9
7 A5A 0.752809 0.908046
8 VMS 0.736264 0.88764
9 54H 0.736264 0.88764
10 TSB 0.728261 0.897727
11 53H 0.728261 0.877778
12 52H 0.717391 0.877778
13 YSA 0.707071 0.920455
14 NVA LMS 0.705263 0.911111
15 G5A 0.7 0.965116
16 NSS 0.694737 0.920455
17 XAH 0.673267 0.853933
18 WSA 0.669811 0.931035
19 8X1 0.639175 0.954545
20 5AS 0.633333 0.898876
21 8PZ 0.631068 0.920455
22 LAD 0.623762 0.852273
23 P5A 0.607843 0.988506
24 LMS 0.602273 0.906977
25 B1U 0.59434 0.831579
26 8Q2 0.575221 0.89011
27 4YB 0.558559 0.921348
28 649 0.552632 0.94382
29 AHX 0.542857 0.8
30 SON 0.541667 0.786517
31 LEU LMS 0.537736 0.827957
32 CA0 0.536082 0.755556
33 7MD 0.535714 0.833333
34 5AL 0.534653 0.764045
35 A 0.532609 0.75
36 AMP 0.532609 0.75
37 5X8 0.530612 0.704545
38 AMP MG 0.526882 0.738636
39 SRP 0.524272 0.806818
40 DSH 0.521277 0.75
41 ADX 0.520408 0.863636
42 SLU 0.520325 0.868132
43 SA8 0.52 0.695652
44 ABM 0.515789 0.733333
45 A2D 0.515789 0.752809
46 45A 0.515789 0.733333
47 KG4 0.515152 0.755556
48 SAH 0.514852 0.727273
49 QA7 0.514286 0.73913
50 SRA 0.510638 0.775281
51 AN2 0.510204 0.764045
52 YLP 0.508621 0.815217
53 5N5 0.505747 0.689655
54 AOC 0.505263 0.674157
55 BA3 0.505155 0.752809
56 A12 0.505155 0.766667
57 AP2 0.505155 0.766667
58 AU1 0.50505 0.755556
59 V2G 0.504854 0.8
60 AMO 0.504673 0.786517
61 SFG 0.5 0.712644
62 AP5 0.5 0.752809
63 ADP 0.5 0.752809
64 ME8 0.5 0.774194
65 ADN 0.5 0.689655
66 5CD 0.5 0.659091
67 XYA 0.5 0.689655
68 RAB 0.5 0.689655
69 TXA 0.5 0.747253
70 NB8 0.5 0.78022
71 B4P 0.5 0.752809
72 YLB 0.495798 0.815217
73 YLC 0.495798 0.833333
74 8QN 0.495327 0.764045
75 9ZA 0.495327 0.75
76 9ZD 0.495327 0.75
77 8LH 0.495238 0.766667
78 GAP 0.495146 0.775281
79 ADP BEF 0.494949 0.75
80 ADP MG 0.494949 0.75
81 AT4 0.494949 0.766667
82 S4M 0.494845 0.712766
83 3DH 0.494624 0.655556
84 AYB 0.491803 0.806452
85 8LE 0.490385 0.73913
86 M33 0.49 0.744444
87 DAL AMP 0.485981 0.744444
88 8LQ 0.485981 0.766667
89 SAI 0.485437 0.7
90 ATP 0.485149 0.752809
91 HEJ 0.485149 0.752809
92 ACP 0.485149 0.755556
93 50T 0.485149 0.725275
94 YLA 0.483607 0.815217
95 EP4 0.483516 0.641304
96 7MC 0.483333 0.815217
97 A4D 0.483146 0.689655
98 3UK 0.481818 0.755556
99 K15 0.481818 0.691489
100 QXP 0.481481 0.844444
101 S7M 0.481132 0.698925
102 SMM 0.481132 0.694737
103 SAM 0.480769 0.698925
104 ANP 0.480769 0.755556
105 AQP 0.480392 0.752809
106 APR 0.480392 0.752809
107 PRX 0.480392 0.736264
108 AR6 0.480392 0.752809
109 5FA 0.480392 0.752809
110 APC 0.480392 0.766667
111 A7D 0.48 0.735632
112 GJV 0.479592 0.714286
113 6RE 0.479167 0.703297
114 DTA 0.478261 0.704545
115 WAQ 0.477477 0.808989
116 J4G 0.477477 0.797753
117 4AD 0.477064 0.777778
118 RUZ 0.477064 0.91954
119 PAJ 0.477064 0.734043
120 EEM 0.47619 0.663158
121 F2R 0.475806 0.795699
122 RBY 0.475728 0.766667
123 ADV 0.475728 0.766667
124 AD9 0.475728 0.736264
125 ATP MG 0.475728 0.75
126 AGS 0.475728 0.777778
127 ADP PO3 0.475728 0.75
128 APC MG 0.475728 0.752809
129 FA5 0.473684 0.786517
130 9K8 0.473214 0.737374
131 62X 0.472727 0.677083
132 DLL 0.472727 0.764045
133 ATF 0.471698 0.728261
134 VO4 ADP 0.471698 0.736264
135 ANP MG 0.471698 0.764045
136 BEF ADP 0.471154 0.733333
137 H1Q 0.470588 0.741573
138 ARG AMP 0.470085 0.784946
139 J7C 0.469388 0.711111
140 OOB 0.46789 0.764045
141 ACQ 0.466667 0.755556
142 T99 0.466667 0.766667
143 TAT 0.466667 0.766667
144 A3S 0.465347 0.724138
145 9SN 0.464912 0.723404
146 R2V 0.464286 0.844444
147 0UM 0.463636 0.725275
148 HQG 0.462963 0.744444
149 TYM 0.46281 0.786517
150 M2T 0.462366 0.645161
151 PTJ 0.460177 0.723404
152 FYA 0.460177 0.764045
153 1ZZ 0.460177 0.755319
154 BIS 0.460177 0.75
155 JNT 0.459459 0.775281
156 00A 0.459459 0.731183
157 KY2 0.458716 0.717391
158 A22 0.458716 0.744444
159 MAP 0.458716 0.73913
160 ALF ADP 0.457944 0.702128
161 MTA 0.457447 0.655556
162 VRT 0.457143 0.711111
163 KYE 0.456897 0.72043
164 RSN 0.45614 0.909091
165 MYR AMP 0.45614 0.736842
166 KB1 0.45614 0.688172
167 RRW 0.45614 0.888889
168 OAD 0.455357 0.755556
169 A3N 0.454545 0.666667
170 25A 0.454545 0.752809
171 OZV 0.454545 0.752809
172 N0B 0.454545 0.815217
173 5SV 0.454545 0.741935
174 YLY 0.453846 0.806452
175 KXW 0.453782 0.733333
176 KH3 0.453782 0.702128
177 6YZ 0.453704 0.755556
178 IOT 0.451613 0.806452
179 PR8 0.451327 0.842697
180 B5V 0.451327 0.747253
181 NWW 0.450549 0.62069
182 ADQ 0.45045 0.755556
183 KYB 0.45045 0.717391
184 A1R 0.45045 0.808989
185 HZ2 0.45 0.736264
186 AAT 0.448598 0.733333
187 JB6 0.447368 0.788889
188 3OD 0.447368 0.755556
189 SXZ 0.447368 0.698925
190 MHZ 0.446602 0.723404
191 48N 0.446281 0.741935
192 MAO 0.445545 0.741935
193 A3G 0.444444 0.735632
194 HY8 0.442623 0.736264
195 ADP BMA 0.442478 0.736264
196 9X8 0.442478 0.758242
197 QXG 0.442478 0.835165
198 A3T 0.442308 0.693182
199 TAD 0.441667 0.771739
200 AMP DBH 0.440678 0.698925
201 V47 0.440367 0.681818
202 ALF ADP 3PG 0.439024 0.715789
203 TXE 0.439024 0.75
204 ZAS 0.438776 0.688889
205 LAQ 0.438017 0.793478
206 A3R 0.4375 0.808989
207 7C5 0.436975 0.677419
208 B5M 0.435897 0.73913
209 B5Y 0.435897 0.73913
210 N5A 0.435644 0.701149
211 KOY 0.434426 0.7
212 LPA AMP 0.434426 0.774194
213 25L 0.431034 0.744444
214 KY5 0.431034 0.730337
215 6V0 0.430894 0.741935
216 NEC 0.43 0.651685
217 RRB 0.429752 0.909091
218 GEK 0.428571 0.741573
219 S8M 0.428571 0.741573
220 4UV 0.428571 0.73913
221 OMR 0.427419 0.747368
222 KY8 0.426087 0.733333
223 F0P 0.424 0.733333
224 KMQ 0.423729 0.728261
225 OZP 0.422764 0.733333
226 EO7 0.421569 0.866667
227 AR6 AR6 0.421488 0.733333
228 4UU 0.421488 0.73913
229 GA7 0.421488 0.747253
230 D3Y 0.419643 0.707865
231 TXD 0.419355 0.75
232 NAX 0.419355 0.763441
233 DND 0.419355 0.747253
234 EU9 0.419355 0.71134
235 NWQ 0.418367 0.606742
236 DQV 0.418033 0.764045
237 SO8 0.416667 0.67033
238 AF3 ADP 3PG 0.416 0.715789
239 N5O 0.415842 0.724138
240 COD 0.415385 0.808511
241 2VA 0.415094 0.677778
242 AHZ 0.414634 0.71875
243 3AM 0.414141 0.738636
244 T5A 0.414062 0.739583
245 Q2V 0.414062 0.706522
246 3NZ 0.413793 0.703297
247 NAD IBO 0.412698 0.752809
248 Q34 0.412698 0.666667
249 Q2M 0.412698 0.698925
250 NAD TDB 0.412698 0.752809
251 ATP A A A 0.411765 0.741573
252 ATP A 0.411765 0.741573
253 U4Y 0.41129 0.722222
254 5AD 0.411111 0.609195
255 AFH 0.409836 0.734043
256 80F 0.409091 0.739583
257 7D5 0.408163 0.722222
258 NAI 0.408 0.731183
259 4UW 0.408 0.715789
260 UP5 0.408 0.73913
261 NVA 2AD 0.407407 0.703297
262 A5D 0.407407 0.704545
263 7D7 0.406593 0.647727
264 GTA 0.406504 0.701031
265 K3E 0.404959 0.673913
266 4TA 0.40458 0.729167
267 Q2P 0.40458 0.666667
268 A2P 0.403846 0.738636
269 A3P 0.403846 0.75
270 594 0.402985 0.864583
271 G3A 0.401639 0.723404
272 4TC 0.401575 0.741935
273 L3W 0.401575 0.747253
274 BT5 0.401515 0.787234
275 V3L 0.4 0.752809
276 K3K 0.4 0.663043
277 CNA 0.4 0.766667
278 67D 0.4 0.9
Similar Ligands (3D)
Ligand no: 1; Ligand: KAA; Similar ligands found: 3
No: Ligand Similarity coefficient
1 GTP 0.8702
2 GNP 0.8631
3 GCP 0.8610
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 6AAD 9TU 17.1533
2 6AAD ATP 17.1533
3 7AP4 RSN 22.029
4 2XGT NSS 28.4058
5 2XGT NSS 28.4058
6 3NEM AMO 40.5797
Pocket No.: 2; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 6AAD 9TU 17.1533
2 6AAD ATP 17.1533
3 2XGT NSS 28.4058
4 2XGT NSS 28.4058
5 3NEM AMO 40.5797
Pocket No.: 3; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 3a5y.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2I4O ATP 6.08696
2 5V59 8X1 10.1449
3 3REU ATP 12.9252
4 2XGT NSS 28.4058
5 3NEM ATP 40.5797
6 3NEM AMO 40.5797
Pocket No.: 4; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 3a5y.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2I4O ATP 6.08696
2 3NEM ATP 40.5797
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