Receptor
PDB id Resolution Class Description Source Keywords
2YVP 1.66 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF NDX2 IN COMPLEX WITH MG2+ AND AMPCPR FR THERMOPHILUS HB8 THERMUS THERMOPHILUS NUDIX PROTEIN ADP-RIBOSE FAD THERMUS THERMOPHILUS HYDROLSTRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STAND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMIINITIATIVE RSGI
Ref.: STRUCTURAL BASIS FOR DIFFERENT SUBSTRATE SPECIFICIT TWO ADP-RIBOSE PYROPHOSPHATASES FROM THERMUS THERMO HB8 J.BACTERIOL. V. 190 1108 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:183;
A:184;
A:185;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
RBY A:186;
Valid;
none;
submit data
557.343 C16 H25 N5 O13 P2 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YVO 1.67 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF NDX2 IN COMPLEX WITH MG2+ AND AMP FROM THERMOPHILUS HB8 THERMUS THERMOPHILUS NUDIX PROTEIN ADP-RIBOSE FAD THERMUS THERMOPHILUS HYDROLSTRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STAND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMIINITIATIVE RSGI
Ref.: STRUCTURAL BASIS FOR DIFFERENT SUBSTRATE SPECIFICIT TWO ADP-RIBOSE PYROPHOSPHATASES FROM THERMUS THERMO HB8 J.BACTERIOL. V. 190 1108 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 2YVP - RBY C16 H25 N5 O13 P2 c1nc(c2c(n....
2 2YVO - AMP C10 H14 N5 O7 P 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 27 families.
1 2YVP - RBY C16 H25 N5 O13 P2 c1nc(c2c(n....
2 2YVO - AMP C10 H14 N5 O7 P 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 25 families.
1 2YVP - RBY C16 H25 N5 O13 P2 c1nc(c2c(n....
2 2YVO - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RBY; Similar ligands found: 328
No: Ligand ECFP6 Tc MDL keys Tc
1 ADV 1 1
2 RBY 1 1
3 A12 0.810811 0.972973
4 AP2 0.810811 0.972973
5 APR 0.805195 0.958904
6 APC 0.805195 0.972973
7 AR6 0.805195 0.958904
8 A 0.743243 0.905405
9 AMP 0.743243 0.905405
10 A2D 0.714286 0.932432
11 45A 0.714286 0.881579
12 ABM 0.714286 0.881579
13 ACP 0.703704 0.959459
14 BA3 0.696203 0.932432
15 M33 0.691358 0.92
16 ACQ 0.690476 0.959459
17 SRA 0.688312 0.858974
18 B4P 0.6875 0.932432
19 AP5 0.6875 0.932432
20 ADP 0.6875 0.932432
21 AT4 0.679012 0.896104
22 AN2 0.679012 0.92
23 PRX 0.674699 0.858974
24 ADX 0.670732 0.841463
25 CA0 0.670732 0.933333
26 AU1 0.670732 0.907895
27 6YZ 0.666667 0.959459
28 50T 0.662651 0.894737
29 HEJ 0.662651 0.932432
30 ATP 0.662651 0.932432
31 KG4 0.662651 0.933333
32 TAD 0.659794 0.923077
33 ADP MG 0.658537 0.905405
34 AQP 0.654762 0.932432
35 5FA 0.654762 0.932432
36 APC MG 0.647059 0.932432
37 ATP MG 0.647059 0.905405
38 AGS 0.647059 0.884615
39 AD9 0.647059 0.907895
40 ADP PO3 0.647059 0.905405
41 SAP 0.647059 0.884615
42 GAP 0.632184 0.883117
43 ANP 0.632184 0.907895
44 TAT 0.632184 0.896104
45 T99 0.632184 0.896104
46 8LE 0.625 0.884615
47 5AL 0.625 0.92
48 SON 0.619048 0.946667
49 ATF 0.617977 0.896104
50 MAP 0.615385 0.884615
51 LMS 0.6125 0.797619
52 8LH 0.611111 0.896104
53 SRP 0.611111 0.921053
54 3OD 0.610526 0.933333
55 9ZD 0.608696 0.873418
56 9ZA 0.608696 0.873418
57 OAD 0.606383 0.933333
58 9X8 0.606383 0.909091
59 HQG 0.604396 0.945946
60 4AD 0.602151 0.934211
61 ADQ 0.602151 0.933333
62 ALF ADP 0.6 0.8375
63 ADP ALF 0.6 0.8375
64 8LQ 0.597826 0.921053
65 A22 0.597826 0.92
66 DAL AMP 0.597826 0.894737
67 DLL 0.595745 0.92
68 ADP VO4 0.593407 0.894737
69 VO4 ADP 0.593407 0.894737
70 OZV 0.591398 0.932432
71 25A 0.591398 0.906667
72 8QN 0.591398 0.92
73 OOB 0.591398 0.92
74 5SV 0.591398 0.839506
75 A2R 0.586957 0.945946
76 PAJ 0.585106 0.875
77 A3R 0.585106 0.922078
78 AMO 0.585106 0.946667
79 A1R 0.585106 0.922078
80 B5V 0.583333 0.896104
81 XYA 0.581081 0.810811
82 ADN 0.581081 0.810811
83 RAB 0.581081 0.810811
84 AHX 0.578947 0.886076
85 00A 0.578947 0.873418
86 AOC 0.578313 0.789474
87 FYA 0.57732 0.894737
88 3UK 0.572917 0.907895
89 DZD 0.572727 0.923077
90 5AS 0.569767 0.752809
91 WAQ 0.56701 0.922078
92 PR8 0.56701 0.8875
93 LAD 0.56701 0.898734
94 5N5 0.565789 0.786667
95 1ZZ 0.561224 0.853659
96 JB6 0.561224 0.873418
97 BIS 0.561224 0.873418
98 ME8 0.561224 0.853659
99 PTJ 0.561224 0.8625
100 TXA 0.561224 0.921053
101 NB8 0.561224 0.910256
102 FA5 0.56 0.921053
103 B5Y 0.56 0.884615
104 5CD 0.558442 0.773333
105 A4D 0.558442 0.786667
106 ADP BMA 0.556701 0.907895
107 25L 0.555556 0.92
108 MYR AMP 0.555556 0.831325
109 A A 0.55102 0.881579
110 M2T 0.55 0.707317
111 9SN 0.55 0.8625
112 G5A 0.549451 0.772727
113 YAP 0.544554 0.909091
114 ATP A A A 0.544554 0.893333
115 B5M 0.544554 0.884615
116 ATP A 0.544554 0.893333
117 A3P 0.54023 0.905405
118 XAH 0.539216 0.853659
119 GA7 0.538462 0.896104
120 AFH 0.538462 0.898734
121 EP4 0.5375 0.725
122 4TC 0.537037 0.910256
123 7D5 0.536585 0.844156
124 TYR AMP 0.533981 0.884615
125 AMP DBH 0.533981 0.883117
126 4UV 0.533981 0.884615
127 H1Q 0.533333 0.868421
128 DQV 0.533333 0.92
129 DTA 0.530864 0.779221
130 3DH 0.53012 0.74359
131 G3A 0.528846 0.8625
132 LAQ 0.528302 0.853659
133 AHZ 0.528302 0.809524
134 OMR 0.527778 0.865854
135 MTA 0.52439 0.74359
136 G5P 0.52381 0.8625
137 ARG AMP 0.52381 0.821429
138 3AM 0.52381 0.866667
139 4UU 0.52381 0.884615
140 LPA AMP 0.523364 0.831325
141 A2P 0.522727 0.891892
142 GTA 0.518868 0.831325
143 NAX 0.518519 0.864198
144 UP5 0.518519 0.884615
145 TXD 0.518519 0.873418
146 4UW 0.518519 0.851852
147 A5A 0.515789 0.77907
148 TSB 0.515464 0.790698
149 TYM 0.513761 0.921053
150 6RE 0.511628 0.731707
151 S4M 0.511364 0.681818
152 SSA 0.510417 0.793103
153 7MD 0.509434 0.876543
154 AR6 AR6 0.509434 0.906667
155 48N 0.509259 0.910256
156 YLP 0.509259 0.855422
157 AP0 0.509091 0.8625
158 PAP 0.505376 0.918919
159 54H 0.505155 0.761364
160 52H 0.505155 0.752809
161 VMS 0.505155 0.761364
162 DND 0.504587 0.921053
163 NXX 0.504587 0.921053
164 6V0 0.504587 0.8625
165 NAI 0.504587 0.873418
166 J7C 0.5 0.740741
167 53H 0.5 0.752809
168 ZAS 0.5 0.7375
169 TXE 0.5 0.873418
170 9K8 0.5 0.709677
171 IMO 0.5 0.866667
172 A3N 0.5 0.75641
173 5CA 0.5 0.793103
174 8X1 0.5 0.747253
175 UPA 0.495495 0.873418
176 YLC 0.495495 0.876543
177 YLB 0.495495 0.855422
178 V3L 0.494737 0.932432
179 2A5 0.494624 0.883117
180 6MZ 0.494382 0.868421
181 7D3 0.494382 0.87013
182 2AM 0.494118 0.88
183 AYB 0.491228 0.845238
184 A4P 0.491071 0.793103
185 P5A 0.490196 0.758242
186 NSS 0.49 0.793103
187 LSS 0.49 0.755556
188 DSZ 0.49 0.813953
189 PPS 0.489583 0.819277
190 ATR 0.489362 0.905405
191 7D4 0.48913 0.87013
192 MAO 0.488889 0.77381
193 DSH 0.488636 0.740741
194 IOT 0.486726 0.845238
195 AF3 ADP 3PG 0.486486 0.851852
196 NVA LMS 0.485149 0.747253
197 5X8 0.483871 0.779221
198 T5A 0.482456 0.855422
199 ADJ 0.482456 0.865854
200 139 0.482456 0.864198
201 YLA 0.482456 0.855422
202 7MC 0.482143 0.855422
203 LEU LMS 0.480392 0.747253
204 CNA 0.478261 0.896104
205 GJV 0.477778 0.722892
206 OVE 0.477273 0.846154
207 KAA 0.475728 0.766667
208 GSU 0.475728 0.793103
209 80F 0.474576 0.855422
210 5AD 0.474359 0.716216
211 F2R 0.474138 0.855422
212 A5D 0.473684 0.779221
213 ITT 0.473118 0.88
214 COD 0.470085 0.825581
215 AMP NAD 0.470085 0.894737
216 NAD 0.470085 0.894737
217 4TA 0.470085 0.821429
218 BTX 0.470085 0.833333
219 HFD 0.46875 0.884615
220 JSQ 0.46875 0.884615
221 SFG 0.468085 0.789474
222 YSA 0.46729 0.772727
223 BT5 0.466102 0.845238
224 SMM 0.464646 0.72093
225 SAM 0.463918 0.72619
226 YLY 0.46281 0.845238
227 M24 0.46281 0.841463
228 A7D 0.462366 0.792208
229 A3D 0.462185 0.883117
230 NAE 0.459016 0.860759
231 7C5 0.458716 0.7875
232 SA8 0.458333 0.743902
233 8PZ 0.457944 0.793103
234 G A A A 0.457627 0.817073
235 MHZ 0.457447 0.712644
236 71V 0.456522 0.85
237 A3G 0.455556 0.792208
238 B1U 0.453704 0.712766
239 SAI 0.453608 0.772152
240 6C6 0.453608 0.871795
241 SAH 0.453608 0.782051
242 A A A 0.451923 0.92
243 PO4 PO4 A A A A PO4 0.451923 0.866667
244 NA7 0.451923 0.946667
245 Y3J 0.451219 0.697368
246 AVV 0.45098 0.910256
247 7D7 0.45 0.736842
248 S7M 0.45 0.72619
249 6IA 0.44898 0.807229
250 J4G 0.447619 0.909091
251 ENQ 0.447619 0.905405
252 WSA 0.447368 0.781609
253 U A 0.446281 0.85
254 NAJ PZO 0.446281 0.817073
255 FB0 0.446154 0.818182
256 A G 0.445378 0.82716
257 EAD 0.444444 0.841463
258 AAT 0.444444 0.722892
259 EEM 0.444444 0.72619
260 6AD 0.444444 0.851852
261 NAQ 0.443548 0.839506
262 KOY 0.442478 0.794872
263 PGS 0.442105 0.82716
264 U A G G 0.441667 0.82716
265 G2P 0.441176 0.898734
266 ZID 0.44 0.883117
267 N0B 0.44 0.855422
268 2SA 0.44 0.921053
269 AV2 0.44 0.857143
270 NEC 0.43956 0.717949
271 D5M 0.43956 0.868421
272 DA 0.43956 0.868421
273 4YB 0.4375 0.775281
274 GEK 0.436893 0.775
275 Z5A 0.436508 0.772727
276 V1N 0.436364 0.906667
277 AAM 0.434783 0.905405
278 3AT 0.434343 0.932432
279 GP2 0.434343 0.898734
280 NAJ PYZ 0.432 0.77907
281 C2R 0.431818 0.868421
282 AMZ 0.431818 0.855263
283 A3S 0.431579 0.802632
284 NO7 0.431373 0.871795
285 G1R 0.431373 0.873418
286 P1H 0.430769 0.821429
287 ARU 0.428571 0.807229
288 101 0.428571 0.844156
289 A U 0.42735 0.8375
290 LQJ 0.427273 0.881579
291 GGZ 0.427184 0.795181
292 6FA 0.425373 0.833333
293 A6D 0.424528 0.717647
294 N5O 0.423913 0.75641
295 AIR 0.423529 0.84
296 6K6 0.423077 0.868421
297 DAT 0.42268 0.894737
298 A3T 0.42268 0.789474
299 649 0.422414 0.758242
300 NIA 0.422222 0.771084
301 DTP 0.42 0.894737
302 NDE 0.419847 0.871795
303 7RA 0.419355 0.893333
304 0UM 0.419048 0.73494
305 8Q2 0.418803 0.766667
306 FDA 0.41791 0.804598
307 FNK 0.417266 0.777778
308 SXZ 0.416667 0.746988
309 62X 0.415094 0.701149
310 N6P 0.415094 0.853333
311 N5A 0.414894 0.730769
312 8BR 0.414894 0.848101
313 NDC 0.413534 0.8625
314 3AD 0.411765 0.797297
315 K15 0.411215 0.717647
316 S8M 0.409524 0.775
317 FAS 0.408759 0.843373
318 SFD 0.408759 0.729167
319 FAD 0.408759 0.843373
320 AS 0.404255 0.825
321 ACK 0.402174 0.826667
322 QQY 0.402174 0.78481
323 7DD 0.402062 0.918919
324 NJP 0.401639 0.884615
325 TM1 0.4 0.747126
326 SLU 0.4 0.744444
327 EO7 0.4 0.761364
328 KB1 0.4 0.73494
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YVO; Ligand: AMP; 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: 2yvo.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2YVO; Ligand: AMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2yvo.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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