-->
Receptor
PDB id Resolution Class Description Source Keywords
3AGO 0.99 Å EC: 3.1.27.4 CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 CO WITH ADENOSINE 3'-MONOPHOSPHATE USTILAGO SPHAEROGENA PURINE-SPECIFIC ENDO-RIBONUCLEASE HYDROLASE
Ref.: ISOMERIZATION MECHANISM OF ASPARTATE TO ISOASPARTAT BY STRUCTURES OF USTILAGO SPHAEROGENA RIBONUCLEASE COMPLEXED WITH ADENOSINE 3'-MONOPHOSPHATE ACTA CRYSTALLOGR.,SECT.D V. 66 843 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3AM A:115;
Valid;
none;
submit data
347.221 C10 H14 N5 O7 P c1nc(...
CA A:116;
A:117;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
CL A:118;
Invalid;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3AHW 1.03 Å EC: 3.1.27.4 CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 CO WITH ADENOSINE 2'-MONOPHOSPHATE USTILAGO SPHAEROGENA PURINE-SPECIFIC ENDO-RIBONUCLEASE HYDROLASE
Ref.: CONFORMATIONAL VARIATION REVEALED BY THE CRYSTAL ST OF RNASE U2A COMPLEXED WITH CA ION AND 2'-ADENYLIC 1.03A RESOLUTION PROTEIN PEPT.LETT. V. 17 1559 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3AGO - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
2 3AHW - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
3 3AGN - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3AGO - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
2 3AHW - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
3 3AGN - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (60)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 6GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1TRP - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
3 5GSP - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
4 7RNT - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
5 1FYS - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
6 1LOV - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
7 6RNT Kd = 4.3 mM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
8 1RGA - G C10 H14 N5 O8 P c1nc2c(n1[....
9 1RLS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
10 1LOW - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
11 1I2F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
12 1DET Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
13 1HZ1 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
14 5BIR Kd = 255 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
15 1FZU - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
16 1B2M - G U34 n/a n/a
17 1BVI - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
18 1I2E - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
19 1G02 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
20 1BIR Kd = 138 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
21 1RNT Kd = 6.5 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
22 3BIR Kd = 112 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
23 1CH0 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
24 1I3I - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
25 4GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
26 2AAD - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
27 5HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
28 3BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
29 3SYU Kd = 50 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
30 1I0V - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
31 1RHL - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
32 1I2G - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
33 1I0X - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
34 1RGK Kd = 49 uM 2AM C10 H14 N5 O7 P c1nc(c2c(n....
35 1I3F - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
36 1LRA - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
37 4HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
38 2RNT - GPG C20 H25 N10 O12 P c1nc2c(n1[....
39 2BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
40 5BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
41 2BIR - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
42 1RGC - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
43 1GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
44 2HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
45 1HYF - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
46 7GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
47 3GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
48 3HOH - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
49 1LOY - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
50 1BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
51 2GSP - SGP C10 H12 N5 O6 P S c1nc2c(n1[....
52 1RGL Kd = 37 uM 2GP C10 H14 N5 O8 P c1nc2c(n1[....
53 1TRQ - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
54 4BU4 - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
55 1RMS - 3GP C10 H14 N5 O8 P c1nc2c(n1[....
56 1RDS - GPC C19 H24 F N8 O11 P c1nc2c(n1[....
57 3AGO - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
58 3AHW - 2AM C10 H14 N5 O7 P c1nc(c2c(n....
59 3AGN - 3AM C10 H14 N5 O7 P c1nc(c2c(n....
60 1FUT - 2GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3AM; Similar ligands found: 373
No: Ligand ECFP6 Tc MDL keys Tc
1 3AM 1 1
2 A3P 0.794118 0.956522
3 PAP 0.72973 0.942857
4 PPS 0.701299 0.835443
5 2AM 0.691176 0.956522
6 ADN 0.640625 0.828571
7 RAB 0.640625 0.828571
8 XYA 0.640625 0.828571
9 A2P 0.626667 0.942029
10 A 0.625 0.956522
11 AMP 0.625 0.956522
12 OVE 0.616438 0.916667
13 7D5 0.605634 0.915493
14 APU 0.581633 0.905405
15 ATR 0.580247 0.928571
16 A2D 0.578947 0.902778
17 ABM 0.578947 0.902778
18 ADP 0.576923 0.929577
19 7D7 0.575758 0.8
20 5N5 0.573529 0.802817
21 SRA 0.573333 0.90411
22 A22 0.569767 0.916667
23 AN2 0.56962 0.916667
24 5CD 0.565217 0.788732
25 A4D 0.565217 0.802817
26 A12 0.564103 0.891892
27 BA3 0.564103 0.902778
28 AP2 0.564103 0.891892
29 AGS 0.560976 0.88
30 SAP 0.560976 0.88
31 B4P 0.556962 0.902778
32 AP5 0.556962 0.902778
33 ATP 0.555556 0.929577
34 HEJ 0.555556 0.929577
35 7D3 0.551282 0.890411
36 AT4 0.55 0.891892
37 SON 0.55 0.891892
38 APC 0.548781 0.891892
39 AQP 0.548781 0.929577
40 5FA 0.548781 0.929577
41 A A A 0.544444 0.864865
42 ADX 0.54321 0.8125
43 AU1 0.54321 0.90411
44 M33 0.54321 0.890411
45 CA0 0.54321 0.878378
46 EP4 0.541667 0.736842
47 A2R 0.54023 0.916667
48 LMS 0.539474 0.790123
49 A A 0.538462 0.929577
50 5AD 0.537313 0.753623
51 ACP 0.536585 0.90411
52 50T 0.536585 0.916667
53 M2T 0.534247 0.717949
54 DTA 0.534247 0.77027
55 101 0.532468 0.942857
56 APR 0.53012 0.902778
57 AR6 0.53012 0.902778
58 PRX 0.53012 0.878378
59 2A5 0.53012 0.90411
60 T99 0.529412 0.891892
61 ANP 0.529412 0.90411
62 TAT 0.529412 0.891892
63 ACQ 0.529412 0.90411
64 Y3J 0.528571 0.732394
65 25A 0.52809 0.929577
66 MTA 0.527027 0.756757
67 A3G 0.525641 0.783784
68 7D4 0.52439 0.890411
69 ADV 0.52381 0.866667
70 AD9 0.52381 0.90411
71 RBY 0.52381 0.866667
72 ADQ 0.522222 0.90411
73 A U 0.519608 0.855263
74 ATF 0.517241 0.891892
75 ATP A A A 0.515789 0.888889
76 3DH 0.513158 0.756757
77 6RE 0.512821 0.766234
78 V3L 0.511628 0.929577
79 6YZ 0.511364 0.90411
80 OOB 0.511111 0.890411
81 NA7 0.51087 0.891892
82 0WD 0.509434 0.857143
83 AOC 0.506329 0.805556
84 ADP PO3 0.505882 0.901408
85 5AL 0.505747 0.890411
86 5X8 0.5 0.746667
87 MAP 0.5 0.88
88 ZAS 0.5 0.75
89 DLL 0.5 0.890411
90 00A 0.5 0.844156
91 3GP 0.5 0.90411
92 PUA 0.5 0.846154
93 5AS 0.5 0.764706
94 PAX 0.495575 0.814815
95 G A A A 0.495327 0.857143
96 25L 0.494737 0.916667
97 ADP BMA 0.494624 0.878378
98 5SV 0.494505 0.833333
99 VO4 ADP 0.494382 0.890411
100 ADP VO4 0.494382 0.890411
101 SRP 0.494382 0.891892
102 GAP 0.494253 0.878378
103 A3S 0.493976 0.794521
104 S4M 0.493827 0.670588
105 DCA 0.490909 0.788235
106 ETB 0.490909 0.797619
107 A5D 0.488372 0.77027
108 MAO 0.487805 0.743902
109 DSH 0.4875 0.730769
110 NEC 0.4875 0.753425
111 3OD 0.484211 0.878378
112 1ZZ 0.484211 0.802469
113 FYA 0.484211 0.890411
114 ALF ADP 0.483146 0.831169
115 ADP ALF 0.483146 0.831169
116 SFG 0.482353 0.733333
117 A3T 0.482353 0.805556
118 COA 0.482143 0.788235
119 0T1 0.482143 0.788235
120 A C A C 0.481818 0.833333
121 A3N 0.481481 0.77027
122 J7C 0.481481 0.776316
123 103 0.481013 0.873239
124 QQY 0.481013 0.875
125 ACK 0.481013 0.926471
126 3AD 0.479452 0.84058
127 3UK 0.478723 0.878378
128 OAD 0.478723 0.878378
129 9X8 0.478723 0.855263
130 9ZA 0.478261 0.868421
131 9ZD 0.478261 0.868421
132 8QN 0.478261 0.890411
133 GJV 0.47561 0.75641
134 WAQ 0.473684 0.844156
135 B5V 0.473684 0.866667
136 AMO 0.473118 0.866667
137 A1R 0.473118 0.868421
138 4AD 0.473118 0.855263
139 A3R 0.473118 0.868421
140 PAJ 0.473118 0.846154
141 SA8 0.471264 0.691358
142 AMX 0.469565 0.797619
143 CAO 0.469565 0.761364
144 COS 0.469565 0.770115
145 30N 0.469565 0.72043
146 FA5 0.469388 0.866667
147 DA 0.469136 0.888889
148 D5M 0.469136 0.888889
149 PTJ 0.46875 0.857143
150 BIS 0.46875 0.868421
151 QQX 0.468354 0.863014
152 AHX 0.468085 0.857143
153 DAL AMP 0.467391 0.864865
154 AV2 0.466667 0.876712
155 G5A 0.465909 0.764706
156 SAH 0.465909 0.727273
157 SAI 0.465909 0.717949
158 SCO 0.465517 0.788235
159 CMX 0.465517 0.788235
160 2VA 0.465116 0.783784
161 CC5 0.464789 0.8
162 ACO 0.461538 0.761364
163 FCX 0.461538 0.761364
164 FAM 0.461538 0.770115
165 3AT 0.460674 0.929577
166 3D1 0.459459 0.780822
167 3L1 0.459459 0.780822
168 9SN 0.459184 0.833333
169 A7D 0.458824 0.783784
170 LAD 0.458333 0.846154
171 PR8 0.458333 0.835443
172 HAX 0.457627 0.770115
173 EEM 0.455556 0.674699
174 B5Y 0.454545 0.855263
175 A G 0.454545 0.844156
176 YAP 0.454545 0.855263
177 NVA 2AD 0.454545 0.74359
178 B5M 0.454545 0.855263
179 FYN 0.453782 0.788235
180 3KK 0.453782 0.770115
181 ME8 0.453608 0.802469
182 TXA 0.453608 0.866667
183 NB8 0.453608 0.833333
184 MHZ 0.453488 0.702381
185 UPA 0.45283 0.868421
186 D3Y 0.451613 0.773333
187 TSB 0.451613 0.761905
188 A5A 0.450549 0.771084
189 U A G G 0.45045 0.844156
190 CA6 0.45 0.697917
191 OXK 0.45 0.770115
192 SOP 0.45 0.770115
193 COK 0.45 0.770115
194 MCD 0.45 0.770115
195 VRT 0.449438 0.753247
196 SO8 0.449438 0.773333
197 MYR AMP 0.44898 0.780488
198 DAT 0.448276 0.864865
199 PO4 PO4 A A A A PO4 0.447917 0.887324
200 CO6 0.446281 0.770115
201 NMX 0.446281 0.728261
202 CMC 0.446281 0.770115
203 1VU 0.446281 0.761364
204 S7M 0.445652 0.674699
205 SSA 0.445652 0.764706
206 SMM 0.445652 0.670588
207 4UV 0.445545 0.855263
208 V1N 0.445545 0.902778
209 ODP 0.445455 0.846154
210 RP1 0.444444 0.851351
211 SAM 0.444444 0.674699
212 SP1 0.444444 0.851351
213 3NZ 0.443299 0.766234
214 SCD 0.442623 0.788235
215 2MC 0.442623 0.736264
216 CAJ 0.442623 0.770115
217 APC G U 0.442478 0.844156
218 U A C C 0.442478 0.820513
219 LAQ 0.442308 0.802469
220 G3A 0.441176 0.857143
221 52H 0.44086 0.744186
222 VMS 0.44086 0.752941
223 54H 0.44086 0.752941
224 NPW 0.440367 0.825
225 IVC 0.439024 0.77907
226 BCO 0.439024 0.770115
227 MLC 0.439024 0.770115
228 1HE 0.439024 0.752809
229 A1S 0.439024 0.770115
230 3HC 0.439024 0.77907
231 JB6 0.438776 0.844156
232 9K8 0.438776 0.681319
233 AFH 0.436893 0.846154
234 4UU 0.436893 0.855263
235 AR6 AR6 0.436893 0.876712
236 G5P 0.436893 0.857143
237 8X1 0.43617 0.738636
238 53H 0.43617 0.744186
239 5CA 0.43617 0.764706
240 GGZ 0.43617 0.7875
241 XAH 0.435644 0.825
242 YE1 0.435484 0.77907
243 MCA 0.435484 0.761364
244 CAA 0.435484 0.77907
245 COO 0.435484 0.770115
246 2BA 0.435294 0.9
247 CMP 0.435294 0.913043
248 A U C C 0.434426 0.833333
249 5J9 0.434343 0.759494
250 A6D 0.43299 0.707317
251 DQV 0.432692 0.890411
252 GTA 0.432692 0.825
253 NJP 0.432432 0.88
254 2CP 0.432 0.761364
255 MC4 0.432 0.728261
256 SCA 0.432 0.770115
257 GEK 0.431579 0.7
258 AMP DBH 0.431373 0.853333
259 TYR AMP 0.431373 0.831169
260 OMR 0.429907 0.792683
261 COW 0.428571 0.761364
262 AS 0.428571 0.842105
263 3CP 0.428571 0.770115
264 CA8 0.428571 0.697917
265 P5A 0.428571 0.730337
266 1GZ 0.428571 0.761364
267 BYC 0.428571 0.770115
268 DTP 0.428571 0.864865
269 HGG 0.428571 0.770115
270 COF 0.428571 0.752809
271 2KQ 0.428571 0.752809
272 IRC 0.428571 0.77907
273 5F1 0.428571 0.716216
274 139 0.427273 0.835443
275 NDP 0.427273 0.857143
276 LSS 0.427083 0.727273
277 DSZ 0.427083 0.744186
278 0UM 0.427083 0.703704
279 NSS 0.427083 0.744186
280 8PZ 0.425743 0.744186
281 BCA 0.425197 0.761364
282 4CA 0.425197 0.761364
283 FAQ 0.425197 0.770115
284 48N 0.424528 0.833333
285 YLP 0.424528 0.804878
286 AAT 0.423913 0.7125
287 NZQ 0.423423 0.846154
288 TXP 0.423423 0.857143
289 MYA 0.423077 0.752809
290 MFK 0.423077 0.752809
291 5F9 0.423077 0.752809
292 ST9 0.423077 0.752809
293 DCC 0.423077 0.752809
294 UCC 0.423077 0.752809
295 ANZ 0.423077 0.807692
296 GA7 0.423077 0.891892
297 NVA LMS 0.42268 0.719101
298 62X 0.42268 0.651163
299 HXC 0.421875 0.752809
300 GRA 0.421875 0.770115
301 A G U 0.420635 0.825
302 UP5 0.420561 0.855263
303 NAX 0.420561 0.8125
304 4UW 0.420561 0.822785
305 DND 0.420561 0.866667
306 NXX 0.420561 0.866667
307 TM1 0.42 0.759036
308 KB1 0.42 0.682927
309 0ET 0.419847 0.752809
310 TAD 0.419048 0.822785
311 TGC 0.418605 0.761364
312 K15 0.418367 0.666667
313 LEU LMS 0.418367 0.719101
314 S8M 0.416667 0.74359
315 TYM 0.416667 0.866667
316 U A A U 0.416667 0.868421
317 XNP 0.415929 0.835443
318 ARJ 0.415584 0.757143
319 1DA 0.415584 0.828571
320 AFX 0.415584 0.706667
321 CCQ 0.415385 0.736264
322 CIC 0.415385 0.770115
323 S0N 0.415385 0.770115
324 2NE 0.415385 0.752809
325 1CZ 0.415385 0.761364
326 CO8 0.415385 0.752809
327 T5A 0.414414 0.783133
328 GSU 0.414141 0.744186
329 KAA 0.414141 0.738636
330 NHM 0.413534 0.752809
331 NHW 0.413534 0.752809
332 UOQ 0.413534 0.752809
333 NOC 0.413333 0.746479
334 DDS 0.413043 0.837838
335 4TC 0.412844 0.833333
336 4CO 0.412214 0.761364
337 0FQ 0.412214 0.770115
338 LPA AMP 0.411215 0.780488
339 CNA 0.410714 0.866667
340 MRS 0.410448 0.752809
341 MRR 0.410448 0.752809
342 7MD 0.409524 0.825
343 ARG AMP 0.409524 0.814815
344 01A 0.409091 0.736264
345 A4P 0.409091 0.807229
346 DG1 0.408333 0.857143
347 1DG 0.408333 0.857143
348 YSA 0.407767 0.744186
349 6V0 0.407407 0.833333
350 NAI 0.407407 0.844156
351 TXD 0.407407 0.844156
352 YNC 0.407407 0.761364
353 ZDA 0.406593 0.849315
354 CS8 0.406015 0.744444
355 WCA 0.406015 0.752809
356 1CV 0.406015 0.770115
357 IOT 0.405405 0.817073
358 U A 0.405172 0.868421
359 A G U U 0.40458 0.825
360 8Z2 0.404412 0.744444
361 TXE 0.40367 0.844156
362 649 0.40367 0.711111
363 HDC 0.402985 0.752809
364 4KX 0.402985 0.744444
365 AHZ 0.401869 0.780488
366 HFQ 0.4 0.752809
367 7C5 0.4 0.779221
368 NAP 0.4 0.90411
369 YLB 0.4 0.804878
370 AP0 0.4 0.833333
371 7MC 0.4 0.804878
372 YLC 0.4 0.825
373 BT5 0.4 0.795181
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3AHW; Ligand: 2AM; Similar sites found with APoc: 35
This union binding pocket(no: 1) in the query (biounit: 3ahw.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5K2M ADP None
2 4KS7 X4Z None
3 3FXU TSU 2.63158
4 3DNT ATP 3.50877
5 2V58 LZJ 3.50877
6 4PU5 ANP 4.38596
7 1VJY 460 4.38596
8 4NFE BEN 5.26316
9 4XZ3 ACP 5.26316
10 3LXK MI1 5.26316
11 4GJ3 0XP 5.26316
12 6C7Y ADP 5.26316
13 1SQL GUN 5.26316
14 1F9A ATP 5.26316
15 1NME 159 7.01754
16 5XVG 8FX 7.01754
17 3NW7 LGV 7.01754
18 2GU8 796 7.01754
19 4WB6 ATP 7.01754
20 4UYW H1S 7.89474
21 4DC2 ADE 7.89474
22 2XK9 XK9 7.89474
23 5UPK ANP 7.89474
24 5LI1 ANP 7.89474
25 6FL8 ADP 7.89474
26 6FL8 TIY 7.89474
27 3DGY 2GP 9.27835
28 2FPU HSO 10.5263
29 5U75 SIA GAL NDG FUC 10.5263
30 6BMN PAP 10.5263
31 2IV2 MGD 10.5263
32 4LO6 SIA GAL 12.2807
33 5TO8 7FM 12.2807
34 3VKX T3 19.2982
35 1RGE 2GP 30.2083
APoc FAQ
Feedback