Receptor
PDB id Resolution Class Description Source Keywords
5ULJ 1.91 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF SCHEFFERSOMYCES STIPITIS RAI1 IN COMPLE (3'-NADP)+ AND CALCIUM ION SCHEFFERSOMYCES STIPITIS (STRAIN ATCC CBS 6054 / NBRC 10063 / NRRL Y-11545) HYDROLASE NADP
Ref.: 5' END NICOTINAMIDE ADENINE DINUCLEOTIDE CAP IN HUM PROMOTES RNA DECAY THROUGH DXO-MEDIATED DENADDING. CELL V. 168 1015 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PPV C:401;
D:401;
Invalid;
Invalid;
none;
none;
submit data
177.975 H4 O7 P2 OP(=O...
CA A:401;
B:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
0WD B:402;
A:402;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0.396;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ULJ 1.91 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF SCHEFFERSOMYCES STIPITIS RAI1 IN COMPLE (3'-NADP)+ AND CALCIUM ION SCHEFFERSOMYCES STIPITIS (STRAIN ATCC CBS 6054 / NBRC 10063 / NRRL Y-11545) HYDROLASE NADP
Ref.: 5' END NICOTINAMIDE ADENINE DINUCLEOTIDE CAP IN HUM PROMOTES RNA DECAY THROUGH DXO-MEDIATED DENADDING. CELL V. 168 1015 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5ULJ - 0WD C21 H30 N7 O17 P3 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 1331 families.
1 5ULJ - 0WD C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5ULJ - 0WD C21 H30 N7 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0WD; Similar ligands found: 297
No: Ligand ECFP6 Tc MDL keys Tc
1 0WD 1 1
2 NDP 0.827273 1
3 NAI 0.814815 0.986842
4 NMN AMP PO4 0.672131 0.948052
5 PAP 0.622642 0.907895
6 AP0 0.609756 0.948718
7 PPS 0.590909 0.811765
8 1DG 0.589552 1
9 DG1 0.589552 1
10 NPW 0.582677 0.962025
11 A3P 0.580952 0.894737
12 NZQ 0.565891 0.987013
13 NAX 0.555556 0.949367
14 80F 0.548872 0.914634
15 A22 0.543103 0.934211
16 DCA 0.540741 0.788889
17 ETB 0.540741 0.797753
18 EAD 0.539568 0.949367
19 0T1 0.532847 0.788889
20 6V0 0.53125 0.974026
21 TXP 0.530303 0.924051
22 PUA 0.525547 0.9125
23 P1H 0.524476 0.925926
24 COA 0.521739 0.788889
25 A2R 0.521368 0.909091
26 A2D 0.518519 0.921053
27 TXE 0.515385 0.935897
28 NA7 0.512397 0.886076
29 XNP 0.511111 0.949367
30 CAO 0.510638 0.763441
31 AMX 0.510638 0.797753
32 COS 0.510638 0.771739
33 30N 0.510638 0.72449
34 3AM 0.509434 0.857143
35 ATR 0.508772 0.894737
36 AGS 0.508772 0.875
37 TXD 0.507692 0.911392
38 SCO 0.507042 0.788889
39 CMX 0.507042 0.788889
40 3OD 0.504065 0.897436
41 ACO 0.503497 0.763441
42 FCX 0.503497 0.763441
43 FAM 0.503497 0.771739
44 OXK 0.503448 0.771739
45 IVC 0.503401 0.78022
46 1VU 0.5 0.763441
47 HAX 0.5 0.771739
48 CAJ 0.496599 0.771739
49 FYN 0.496552 0.788889
50 3KK 0.496552 0.771739
51 HQG 0.495798 0.909091
52 BA3 0.495495 0.921053
53 IRC 0.493333 0.78022
54 A1S 0.493243 0.771739
55 3HC 0.493243 0.78022
56 MLC 0.493243 0.771739
57 1HE 0.493243 0.755319
58 BCO 0.493243 0.771739
59 MCD 0.493151 0.771739
60 YZS 0.493151 0.70297
61 CA6 0.493151 0.70297
62 SOP 0.493151 0.771739
63 COK 0.493151 0.771739
64 KGP 0.493151 0.70297
65 NJP 0.492647 0.923077
66 HEJ 0.491228 0.921053
67 ATP 0.491228 0.921053
68 ADP 0.491071 0.921053
69 AP5 0.491071 0.921053
70 B4P 0.491071 0.921053
71 SO5 0.489933 0.696078
72 CAA 0.489933 0.78022
73 LCV 0.489933 0.696078
74 MCA 0.489933 0.763441
75 NMX 0.489796 0.731959
76 CO6 0.489796 0.771739
77 CMC 0.489796 0.771739
78 NAJ PZO 0.489209 0.924051
79 AQP 0.486957 0.921053
80 5FA 0.486957 0.921053
81 AR6 0.486957 0.896104
82 APR 0.486957 0.896104
83 AN2 0.486726 0.909091
84 MC4 0.486667 0.787234
85 SCD 0.486486 0.788889
86 2MC 0.486486 0.795699
87 APU 0.485075 0.923077
88 HGG 0.483444 0.771739
89 KGJ 0.483221 0.72449
90 9BG 0.481752 0.876543
91 YE1 0.48 0.8
92 COO 0.48 0.791209
93 PAX 0.479167 0.902439
94 50T 0.478261 0.884615
95 HXC 0.477124 0.755319
96 SCA 0.476821 0.771739
97 YXS 0.476821 0.70297
98 2CP 0.476821 0.763441
99 YXR 0.476821 0.70297
100 25L 0.47619 0.934211
101 OAD 0.475806 0.897436
102 NAJ PYZ 0.475524 0.879518
103 SRP 0.475 0.8625
104 ANP 0.474576 0.897436
105 KFV 0.473684 0.71
106 KGA 0.473684 0.717172
107 CA8 0.473684 0.72
108 UP5 0.473684 0.948052
109 3CP 0.473684 0.771739
110 COW 0.473684 0.782609
111 COF 0.473684 0.755319
112 2KQ 0.473684 0.755319
113 AT4 0.473684 0.886076
114 BYC 0.473684 0.791209
115 1GZ 0.473684 0.782609
116 4AD 0.471545 0.875
117 ADQ 0.471545 0.897436
118 A1R 0.471545 0.841463
119 1CZ 0.470968 0.763441
120 N9V 0.470968 0.802198
121 CO8 0.470968 0.755319
122 4CA 0.470588 0.782609
123 BCA 0.470588 0.782609
124 FAQ 0.470588 0.791209
125 AD9 0.470085 0.897436
126 M33 0.469565 0.884615
127 CA0 0.469565 0.897436
128 A2P 0.469027 0.881579
129 ATP A A A 0.46875 0.883117
130 ATP A 0.46875 0.883117
131 HDC 0.468354 0.755319
132 4KX 0.468354 0.824176
133 UCC 0.467949 0.755319
134 5F9 0.467949 0.755319
135 ST9 0.467949 0.755319
136 MFK 0.467949 0.755319
137 DCC 0.467949 0.755319
138 MYA 0.467949 0.755319
139 GRA 0.467532 0.771739
140 8LQ 0.467213 0.8625
141 ADJ 0.467153 0.879518
142 ACP 0.465517 0.897436
143 KG4 0.465517 0.897436
144 0ET 0.464968 0.755319
145 TGC 0.464516 0.763441
146 9X8 0.464 0.851852
147 25A 0.463415 0.921053
148 J5H 0.4625 0.791209
149 ACQ 0.462185 0.897436
150 DQV 0.462121 0.934211
151 CS8 0.462025 0.747368
152 CIC 0.461538 0.771739
153 2NE 0.461538 0.774194
154 2A5 0.461538 0.85
155 PRX 0.461538 0.82716
156 S0N 0.461538 0.791209
157 CCQ 0.461538 0.739583
158 A3R 0.459677 0.841463
159 UOQ 0.459119 0.755319
160 NHW 0.459119 0.755319
161 NHM 0.459119 0.755319
162 0FQ 0.458599 0.791209
163 4CO 0.458599 0.782609
164 5AL 0.458333 0.884615
165 ADX 0.456897 0.811765
166 MRR 0.45625 0.755319
167 MRS 0.45625 0.755319
168 00A 0.456 0.864198
169 4TC 0.455882 0.924051
170 01A 0.455696 0.757895
171 QA7 0.455285 0.851852
172 YNC 0.453416 0.782609
173 1CV 0.45283 0.771739
174 WCA 0.45283 0.793478
175 F8G 0.451807 0.797872
176 OOB 0.451613 0.909091
177 6YZ 0.45082 0.897436
178 8LH 0.45082 0.8625
179 8Z2 0.450617 0.765957
180 AMP 0.45045 0.894737
181 A 0.45045 0.894737
182 ODP 0.45 0.936709
183 WAQ 0.448819 0.841463
184 LAD 0.448819 0.821429
185 OMR 0.448529 0.813953
186 AMO 0.448 0.886076
187 PAJ 0.448 0.843373
188 NDP DTT 0.447368 0.891566
189 HFQ 0.447205 0.774194
190 UBG 0.446541 0.847059
191 8LE 0.446281 0.851852
192 FA5 0.446154 0.886076
193 2AM 0.445455 0.87013
194 FYA 0.445312 0.860759
195 1ZZ 0.445312 0.802326
196 YLP 0.444444 0.784091
197 DAK 0.444444 0.784946
198 JNT 0.444444 0.873418
199 DLL 0.444444 0.909091
200 7D4 0.444444 0.8375
201 CNA 0.442857 0.910256
202 ATF 0.442623 0.886076
203 DND 0.441176 0.910256
204 3UK 0.440945 0.897436
205 8QN 0.44 0.884615
206 UCA 0.439306 0.774194
207 TYM 0.437956 0.886076
208 B5V 0.4375 0.886076
209 PR8 0.4375 0.811765
210 01K 0.437126 0.771739
211 APC 0.436975 0.886076
212 NHQ 0.436364 0.78022
213 B5Y 0.435115 0.875
214 B5M 0.435115 0.875
215 KMQ 0.435115 0.886076
216 7D3 0.434783 0.8375
217 YLB 0.434783 0.784091
218 COT 0.434524 0.791209
219 NB8 0.434109 0.853659
220 BIS 0.434109 0.864198
221 PTJ 0.434109 0.853659
222 ME8 0.434109 0.802326
223 48N 0.433824 0.853659
224 NAP 0.432432 0.922078
225 38V 0.432432 0.86747
226 LQJ 0.431818 0.871795
227 1HA 0.431138 0.774194
228 CA3 0.429412 0.791209
229 OZV 0.428571 0.896104
230 5SV 0.428571 0.788235
231 9SN 0.427481 0.853659
232 LAQ 0.426471 0.802326
233 T99 0.42623 0.886076
234 TAT 0.42623 0.886076
235 45A 0.426087 0.848101
236 ABM 0.426087 0.848101
237 COA FLC 0.425676 0.758242
238 T5A 0.425532 0.914634
239 139 0.425532 0.901235
240 RMW 0.425287 0.774194
241 L3W 0.42446 0.960526
242 UPA 0.42446 0.935897
243 YLC 0.42446 0.823529
244 SON 0.423729 0.886076
245 62F 0.42236 0.823529
246 4UU 0.422222 0.948052
247 AHX 0.421875 0.853659
248 SRA 0.421053 0.85
249 AMP MG 0.421053 0.857143
250 4UW 0.42029 0.9125
251 AU1 0.420168 0.897436
252 F2R 0.41958 0.825581
253 A12 0.418803 0.886076
254 AP2 0.418803 0.886076
255 9ZA 0.417323 0.864198
256 9ZD 0.417323 0.864198
257 NA0 0.417219 0.910256
258 7L1 0.417219 0.763441
259 CA5 0.417143 0.757895
260 COD 0.416667 0.777778
261 OXT 0.416216 0.742268
262 YLA 0.415493 0.804598
263 GAP 0.414634 0.85
264 DTP 0.414634 0.8375
265 BT5 0.413793 0.795455
266 AYB 0.412587 0.775281
267 TXA 0.412214 0.886076
268 AFH 0.411765 0.843373
269 ADP BEF 0.411765 0.87013
270 ADP MG 0.411765 0.87013
271 V2G 0.41129 0.853659
272 7D5 0.410714 0.8125
273 TAP 0.410596 0.864198
274 ATP MG 0.409836 0.87013
275 ADP PO3 0.409836 0.87013
276 DAL AMP 0.409449 0.860759
277 AV2 0.408 0.848101
278 ANP MG 0.408 0.860759
279 ADP BMA 0.407692 0.873418
280 4UV 0.407407 0.948052
281 NAD 0.406897 0.909091
282 93P 0.40678 0.782609
283 BEF ADP 0.406504 0.848101
284 BSJ 0.405405 0.765957
285 CO7 0.405063 0.791209
286 BUA COA 0.405063 0.741935
287 DAT 0.404959 0.8375
288 G3A 0.404412 0.9
289 DZD 0.40411 0.865854
290 93M 0.403315 0.782609
291 3AT 0.403226 0.896104
292 YLY 0.402685 0.775281
293 G5P 0.40146 0.9
294 A4P 0.401408 0.892857
295 XAH 0.4 0.802326
296 D4F 0.4 0.823529
297 NAE 0.4 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: 0WD; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ULJ; Ligand: 0WD; 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: 5ulj.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5ULJ; Ligand: 0WD; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 5ulj.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 6WUK COA 41.8953
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