Receptor
PDB id Resolution Class Description Source Keywords
3AGN 0.96 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;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
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: 358
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 XYA 0.640625 0.828571
7 ADN 0.640625 0.828571
8 RAB 0.640625 0.828571
9 A2P 0.626667 0.942029
10 AMP 0.625 0.956522
11 A 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 ABM 0.578947 0.902778
17 A2D 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 AMP MG 0.565789 0.876712
25 A4D 0.565217 0.802817
26 5CD 0.565217 0.788732
27 A12 0.564103 0.891892
28 AP2 0.564103 0.891892
29 BA3 0.564103 0.902778
30 SAP 0.560976 0.88
31 AGS 0.560976 0.88
32 AP5 0.556962 0.902778
33 B4P 0.556962 0.902778
34 BEF ADP 0.555556 0.842105
35 ADP BEF 0.555556 0.842105
36 ATP 0.555556 0.929577
37 7D3 0.551282 0.890411
38 SON 0.55 0.891892
39 APC 0.548781 0.891892
40 AQP 0.548781 0.929577
41 5FA 0.548781 0.929577
42 A A A 0.544444 0.864865
43 M33 0.54321 0.890411
44 CA0 0.54321 0.878378
45 AU1 0.54321 0.90411
46 ADX 0.54321 0.8125
47 ADP MG 0.54321 0.864865
48 EP4 0.541667 0.736842
49 A2R 0.54023 0.916667
50 A A 0.538462 0.929577
51 5AD 0.537313 0.753623
52 ACP 0.536585 0.90411
53 50T 0.536585 0.916667
54 M2T 0.534247 0.717949
55 DTA 0.534247 0.77027
56 101 0.532468 0.942857
57 AR6 0.53012 0.902778
58 APR 0.53012 0.902778
59 PRX 0.53012 0.878378
60 2A5 0.53012 0.90411
61 ACQ 0.529412 0.90411
62 TAT 0.529412 0.891892
63 ANP 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 RBY 0.52381 0.866667
70 AD9 0.52381 0.90411
71 ADV 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 OOB 0.511111 0.890411
80 NA7 0.51087 0.891892
81 0WD 0.509434 0.857143
82 AOC 0.506329 0.805556
83 ADP PO3 0.505882 0.901408
84 5AL 0.505747 0.890411
85 00A 0.5 0.844156
86 MAP 0.5 0.88
87 DLL 0.5 0.890411
88 PUA 0.5 0.846154
89 5X8 0.5 0.746667
90 ZAS 0.5 0.75
91 3GP 0.5 0.90411
92 5AS 0.5 0.764706
93 ATP MG 0.5 0.864865
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 SRP 0.494382 0.891892
100 ADP VO4 0.494382 0.890411
101 VO4 ADP 0.494382 0.890411
102 GAP 0.494253 0.878378
103 A3S 0.493976 0.794521
104 S4M 0.493827 0.670588
105 ETB 0.490909 0.797619
106 DCA 0.490909 0.788235
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 A3T 0.482353 0.805556
117 SFG 0.482353 0.733333
118 COA 0.482143 0.788235
119 0T1 0.482143 0.788235
120 J7C 0.481481 0.776316
121 A3N 0.481481 0.77027
122 103 0.481013 0.873239
123 QQY 0.481013 0.875
124 ACK 0.481013 0.926471
125 3AD 0.479452 0.84058
126 OAD 0.478723 0.878378
127 3UK 0.478723 0.878378
128 8QN 0.478261 0.890411
129 ANP MG 0.477778 0.855263
130 GJV 0.47561 0.75641
131 WAQ 0.473684 0.844156
132 4AD 0.473118 0.855263
133 PAJ 0.473118 0.846154
134 AMO 0.473118 0.866667
135 A1R 0.473118 0.868421
136 NVA 2AD 0.471264 0.75
137 SA8 0.471264 0.691358
138 30N 0.469565 0.72043
139 CAO 0.469565 0.761364
140 AMX 0.469565 0.797619
141 COS 0.469565 0.770115
142 FA5 0.469388 0.866667
143 DA 0.469136 0.888889
144 D5M 0.469136 0.888889
145 BIS 0.46875 0.868421
146 PTJ 0.46875 0.857143
147 QQX 0.468354 0.863014
148 AHX 0.468085 0.857143
149 DAL AMP 0.467391 0.864865
150 AV2 0.466667 0.876712
151 G5A 0.465909 0.764706
152 SAI 0.465909 0.717949
153 SAH 0.465909 0.727273
154 CMX 0.465517 0.788235
155 SCO 0.465517 0.788235
156 2VA 0.465116 0.783784
157 CC5 0.464789 0.8
158 ACO 0.461538 0.761364
159 FAM 0.461538 0.770115
160 FCX 0.461538 0.761364
161 3AT 0.460674 0.929577
162 3L1 0.459459 0.780822
163 3D1 0.459459 0.780822
164 9SN 0.459184 0.833333
165 A7D 0.458824 0.783784
166 LAD 0.458333 0.846154
167 PR8 0.458333 0.835443
168 HAX 0.457627 0.770115
169 EEM 0.455556 0.674699
170 YAP 0.454545 0.855263
171 FYN 0.453782 0.788235
172 3KK 0.453782 0.770115
173 TXA 0.453608 0.866667
174 NB8 0.453608 0.833333
175 ME8 0.453608 0.802469
176 MHZ 0.453488 0.702381
177 UPA 0.45283 0.868421
178 TSB 0.451613 0.761905
179 D3Y 0.451613 0.773333
180 A5A 0.450549 0.771084
181 U A G G 0.45045 0.844156
182 SOP 0.45 0.770115
183 CA6 0.45 0.697917
184 COK 0.45 0.770115
185 OXK 0.45 0.770115
186 MCD 0.45 0.770115
187 VRT 0.449438 0.753247
188 SO8 0.449438 0.773333
189 MYR AMP 0.44898 0.780488
190 DAT 0.448276 0.864865
191 PO4 PO4 A A A A PO4 0.447917 0.887324
192 CO6 0.446281 0.770115
193 1VU 0.446281 0.761364
194 CMC 0.446281 0.770115
195 NMX 0.446281 0.728261
196 S7M 0.445652 0.674699
197 SSA 0.445652 0.764706
198 SMM 0.445652 0.670588
199 V1N 0.445545 0.902778
200 4UV 0.445545 0.855263
201 ODP 0.445455 0.846154
202 SP1 0.444444 0.851351
203 SAM 0.444444 0.674699
204 RP1 0.444444 0.851351
205 3NZ 0.443299 0.766234
206 2MC 0.442623 0.736264
207 SCD 0.442623 0.788235
208 CAJ 0.442623 0.770115
209 APC G U 0.442478 0.844156
210 U A C C 0.442478 0.820513
211 LAQ 0.442308 0.802469
212 G3A 0.441176 0.857143
213 VMS 0.44086 0.752941
214 54H 0.44086 0.752941
215 52H 0.44086 0.744186
216 NPW 0.440367 0.825
217 1HE 0.439024 0.752809
218 IVC 0.439024 0.77907
219 BCO 0.439024 0.770115
220 3HC 0.439024 0.77907
221 MLC 0.439024 0.770115
222 A1S 0.439024 0.770115
223 JB6 0.438776 0.844156
224 G5P 0.436893 0.857143
225 AFH 0.436893 0.846154
226 AR6 AR6 0.436893 0.876712
227 4UU 0.436893 0.855263
228 GGZ 0.43617 0.7875
229 5CA 0.43617 0.764706
230 53H 0.43617 0.744186
231 XAH 0.435644 0.825
232 TYR AMP 0.435644 0.842105
233 MCA 0.435484 0.761364
234 YE1 0.435484 0.77907
235 CAA 0.435484 0.77907
236 COO 0.435484 0.770115
237 2BA 0.435294 0.9
238 CMP 0.435294 0.913043
239 A U C C 0.434426 0.833333
240 5J9 0.434343 0.759494
241 A6D 0.43299 0.707317
242 GTA 0.432692 0.825
243 NJP 0.432432 0.88
244 2CP 0.432 0.761364
245 MC4 0.432 0.728261
246 SCA 0.432 0.770115
247 GEK 0.431579 0.7
248 AMP DBH 0.431373 0.853333
249 OMR 0.429907 0.792683
250 COF 0.428571 0.752809
251 DTP 0.428571 0.864865
252 HGG 0.428571 0.770115
253 1GZ 0.428571 0.761364
254 AS 0.428571 0.842105
255 3CP 0.428571 0.770115
256 IRC 0.428571 0.77907
257 CA8 0.428571 0.697917
258 P5A 0.428571 0.730337
259 5F1 0.428571 0.716216
260 BYC 0.428571 0.770115
261 COW 0.428571 0.761364
262 2KQ 0.428571 0.752809
263 139 0.427273 0.835443
264 NDP 0.427273 0.857143
265 NSS 0.427083 0.744186
266 DSZ 0.427083 0.744186
267 0UM 0.427083 0.703704
268 LSS 0.427083 0.727273
269 FAQ 0.425197 0.770115
270 4CA 0.425197 0.761364
271 BCA 0.425197 0.761364
272 YLP 0.424528 0.804878
273 48N 0.424528 0.833333
274 AAT 0.423913 0.7125
275 NZQ 0.423423 0.846154
276 TXP 0.423423 0.857143
277 UCC 0.423077 0.752809
278 ANZ 0.423077 0.807692
279 DCC 0.423077 0.752809
280 MYA 0.423077 0.752809
281 ST9 0.423077 0.752809
282 MFK 0.423077 0.752809
283 5F9 0.423077 0.752809
284 NVA LMS 0.42268 0.727273
285 62X 0.42268 0.651163
286 GRA 0.421875 0.770115
287 HXC 0.421875 0.752809
288 A G U 0.420635 0.825
289 UP5 0.420561 0.855263
290 DND 0.420561 0.866667
291 NAX 0.420561 0.8125
292 NXX 0.420561 0.866667
293 4UW 0.420561 0.822785
294 TM1 0.42 0.759036
295 KB1 0.42 0.682927
296 0ET 0.419847 0.752809
297 TAD 0.419048 0.822785
298 TGC 0.418605 0.761364
299 K15 0.418367 0.666667
300 LEU LMS 0.418367 0.727273
301 TYM 0.416667 0.866667
302 S8M 0.416667 0.74359
303 U A A U 0.416667 0.868421
304 XNP 0.415929 0.835443
305 AFX 0.415584 0.706667
306 1DA 0.415584 0.828571
307 ARJ 0.415584 0.757143
308 S0N 0.415385 0.770115
309 CO8 0.415385 0.752809
310 1CZ 0.415385 0.761364
311 CCQ 0.415385 0.736264
312 2NE 0.415385 0.752809
313 CIC 0.415385 0.770115
314 T5A 0.414414 0.783133
315 GSU 0.414141 0.744186
316 KAA 0.414141 0.738636
317 NHW 0.413534 0.752809
318 UOQ 0.413534 0.752809
319 NHM 0.413534 0.752809
320 NOC 0.413333 0.746479
321 DDS 0.413043 0.837838
322 4TC 0.412844 0.833333
323 0FQ 0.412214 0.770115
324 4CO 0.412214 0.761364
325 LPA AMP 0.411215 0.780488
326 CNA 0.410714 0.866667
327 MRR 0.410448 0.752809
328 MRS 0.410448 0.752809
329 7MD 0.409524 0.825
330 01A 0.409091 0.736264
331 A4P 0.409091 0.807229
332 1DG 0.408333 0.857143
333 DG1 0.408333 0.857143
334 YSA 0.407767 0.744186
335 TXD 0.407407 0.844156
336 6V0 0.407407 0.833333
337 NAI 0.407407 0.844156
338 YNC 0.407407 0.761364
339 ZDA 0.406593 0.849315
340 CS8 0.406015 0.744444
341 1CV 0.406015 0.770115
342 WCA 0.406015 0.752809
343 IOT 0.405405 0.817073
344 8Z2 0.404412 0.744444
345 649 0.40367 0.711111
346 TXE 0.40367 0.844156
347 4KX 0.402985 0.744444
348 HDC 0.402985 0.752809
349 AHZ 0.401869 0.780488
350 ARG AMP 0.401869 0.814815
351 BT5 0.4 0.795181
352 7MC 0.4 0.804878
353 AP0 0.4 0.833333
354 YLB 0.4 0.804878
355 YLC 0.4 0.825
356 HFQ 0.4 0.752809
357 7C5 0.4 0.779221
358 NAP 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3AHW; Ligand: 2AM; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 3ahw.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NME 159 0.006818 0.43581 7.01754
2 3NW7 LGV 0.01681 0.42151 7.01754
3 4UYW H1S 0.02199 0.4413 7.89474
4 2X4Z X4Z 0.0173 0.41112 8.77193
5 3DGY 2GP 0.0007909 0.47243 9.27835
6 1GOY 3GP 0.0005689 0.416 9.64912
7 5U75 SIA GAL NDG FUC 0.01505 0.4083 10.5263
8 1RGE 2GP 0.0005695 0.47833 30.2083
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