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 28 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 26 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 23 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 (2D)
Ligand no: 1; Ligand: RBY; Similar ligands found: 350
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 AR6 0.805195 0.958904
7 APC 0.805195 0.972973
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 AMP MG 0.710526 0.891892
14 ACP 0.703704 0.959459
15 BA3 0.696203 0.932432
16 M33 0.691358 0.92
17 ACQ 0.690476 0.959459
18 SRA 0.688312 0.858974
19 B4P 0.6875 0.932432
20 ADP 0.6875 0.932432
21 AP5 0.6875 0.932432
22 AT4 0.679012 0.896104
23 AN2 0.679012 0.92
24 PRX 0.674699 0.858974
25 ADX 0.670732 0.841463
26 AU1 0.670732 0.907895
27 CA0 0.670732 0.933333
28 6YZ 0.666667 0.959459
29 HEJ 0.662651 0.932432
30 50T 0.662651 0.894737
31 KG4 0.662651 0.933333
32 ATP 0.662651 0.932432
33 TAD 0.659794 0.923077
34 ADP BEF 0.658537 0.905405
35 ADP MG 0.658537 0.905405
36 AQP 0.654762 0.932432
37 5FA 0.654762 0.932432
38 AGS 0.647059 0.884615
39 ADP PO3 0.647059 0.905405
40 ATP MG 0.647059 0.905405
41 APC MG 0.647059 0.932432
42 AD9 0.647059 0.907895
43 T99 0.632184 0.896104
44 ANP 0.632184 0.907895
45 GAP 0.632184 0.883117
46 TAT 0.632184 0.896104
47 V2G 0.625 0.886076
48 5AL 0.625 0.92
49 8LE 0.625 0.884615
50 BEF ADP 0.62069 0.881579
51 SON 0.619048 0.946667
52 ATF 0.617977 0.896104
53 MAP 0.615385 0.884615
54 QA7 0.615385 0.884615
55 LMS 0.6125 0.797619
56 SRP 0.611111 0.921053
57 8LH 0.611111 0.896104
58 3OD 0.610526 0.933333
59 9ZA 0.608696 0.873418
60 9ZD 0.608696 0.873418
61 9X8 0.606383 0.909091
62 OAD 0.606383 0.933333
63 HQG 0.604396 0.945946
64 4AD 0.602151 0.934211
65 ADQ 0.602151 0.933333
66 ANP MG 0.6 0.894737
67 ALF ADP 0.6 0.8375
68 VO4 ADP 0.6 0.883117
69 DAL AMP 0.597826 0.894737
70 A22 0.597826 0.92
71 8LQ 0.597826 0.921053
72 JNT 0.595745 0.933333
73 DLL 0.595745 0.92
74 5SV 0.591398 0.839506
75 OZV 0.591398 0.932432
76 OOB 0.591398 0.92
77 25A 0.591398 0.906667
78 8QN 0.591398 0.92
79 A2R 0.586957 0.945946
80 A1R 0.585106 0.922078
81 PAJ 0.585106 0.875
82 A3R 0.585106 0.922078
83 AMO 0.585106 0.946667
84 B5V 0.583333 0.896104
85 RAB 0.581081 0.810811
86 ADN 0.581081 0.810811
87 XYA 0.581081 0.810811
88 00A 0.578947 0.873418
89 AHX 0.578947 0.886076
90 AOC 0.578313 0.789474
91 FYA 0.57732 0.894737
92 KMQ 0.575758 0.921053
93 3UK 0.572917 0.907895
94 DZD 0.572727 0.923077
95 5AS 0.569767 0.752809
96 WAQ 0.56701 0.922078
97 LAD 0.56701 0.898734
98 PR8 0.56701 0.8875
99 O02 0.566667 0.935065
100 5N5 0.565789 0.786667
101 JB6 0.561224 0.873418
102 NB8 0.561224 0.910256
103 ME8 0.561224 0.853659
104 1ZZ 0.561224 0.853659
105 BIS 0.561224 0.873418
106 TXA 0.561224 0.921053
107 PTJ 0.561224 0.8625
108 B5Y 0.56 0.884615
109 FA5 0.56 0.921053
110 A4D 0.558442 0.786667
111 5CD 0.558442 0.773333
112 ADP BMA 0.556701 0.907895
113 25L 0.555556 0.92
114 MYR AMP 0.555556 0.831325
115 M2T 0.55 0.707317
116 9SN 0.55 0.8625
117 G5A 0.549451 0.772727
118 ATP A A A 0.544554 0.893333
119 ATP A 0.544554 0.893333
120 B5M 0.544554 0.884615
121 A3P 0.54023 0.905405
122 XAH 0.539216 0.853659
123 GA7 0.538462 0.896104
124 AFH 0.538462 0.898734
125 EP4 0.5375 0.725
126 4TC 0.537037 0.910256
127 7D5 0.536585 0.844156
128 AMP DBH 0.533981 0.883117
129 4UV 0.533981 0.884615
130 H1Q 0.533333 0.868421
131 DQV 0.533333 0.92
132 DTA 0.530864 0.779221
133 3DH 0.53012 0.74359
134 G3A 0.528846 0.8625
135 LAQ 0.528302 0.853659
136 AHZ 0.528302 0.809524
137 OMR 0.527778 0.865854
138 MTA 0.52439 0.74359
139 4UU 0.52381 0.884615
140 ARG AMP 0.52381 0.821429
141 G5P 0.52381 0.8625
142 3AM 0.52381 0.866667
143 LPA AMP 0.523364 0.831325
144 L3W 0.522936 0.896104
145 A2P 0.522727 0.891892
146 GTA 0.518868 0.831325
147 TXD 0.518519 0.873418
148 4UW 0.518519 0.851852
149 UP5 0.518519 0.884615
150 NAX 0.518519 0.864198
151 A5A 0.515789 0.77907
152 TSB 0.515464 0.790698
153 TYM 0.513761 0.921053
154 6RE 0.511628 0.731707
155 S4M 0.511364 0.681818
156 SSA 0.510417 0.793103
157 7MD 0.509434 0.876543
158 AR6 AR6 0.509434 0.906667
159 YLP 0.509259 0.855422
160 48N 0.509259 0.910256
161 AP0 0.509091 0.8625
162 PAP 0.505376 0.918919
163 VMS 0.505155 0.761364
164 52H 0.505155 0.752809
165 54H 0.505155 0.761364
166 6V0 0.504587 0.8625
167 NAI 0.504587 0.873418
168 DND 0.504587 0.921053
169 A3N 0.5 0.75641
170 5CA 0.5 0.793103
171 38V 0.5 0.9
172 TXE 0.5 0.873418
173 ZAS 0.5 0.7375
174 9K8 0.5 0.709677
175 8X1 0.5 0.747253
176 IMO 0.5 0.866667
177 53H 0.5 0.752809
178 J7C 0.5 0.740741
179 YLB 0.495495 0.855422
180 YLC 0.495495 0.876543
181 UPA 0.495495 0.873418
182 V3L 0.494737 0.932432
183 2A5 0.494624 0.883117
184 7D3 0.494382 0.87013
185 6MZ 0.494382 0.868421
186 2AM 0.494118 0.88
187 AYB 0.491228 0.845238
188 A4P 0.491071 0.793103
189 P5A 0.490196 0.758242
190 DSZ 0.49 0.813953
191 LSS 0.49 0.755556
192 NSS 0.49 0.793103
193 PPS 0.489583 0.819277
194 ATR 0.489362 0.905405
195 7D4 0.48913 0.87013
196 MAO 0.488889 0.77381
197 DSH 0.488636 0.740741
198 IOT 0.486726 0.845238
199 ALF ADP 3PG 0.486486 0.851852
200 AF3 ADP 3PG 0.486486 0.851852
201 O05 0.485437 0.857143
202 NVA LMS 0.485149 0.747253
203 5X8 0.483871 0.779221
204 ADJ 0.482456 0.865854
205 YLA 0.482456 0.855422
206 139 0.482456 0.864198
207 T5A 0.482456 0.855422
208 NAD IBO 0.482143 0.881579
209 7MC 0.482143 0.855422
210 NAD TDB 0.482143 0.881579
211 NWW 0.481481 0.72973
212 LEU LMS 0.480392 0.744444
213 CNA 0.478261 0.896104
214 GJV 0.477778 0.722892
215 OVE 0.477273 0.846154
216 KAA 0.475728 0.766667
217 GSU 0.475728 0.793103
218 80F 0.474576 0.855422
219 5AD 0.474359 0.716216
220 F2R 0.474138 0.855422
221 A5D 0.473684 0.779221
222 ITT 0.473118 0.88
223 4TA 0.470085 0.821429
224 AMP NAD 0.470085 0.894737
225 BTX 0.470085 0.833333
226 NAD 0.470085 0.894737
227 COD 0.470085 0.825581
228 JSQ 0.46875 0.884615
229 HFD 0.46875 0.884615
230 SFG 0.468085 0.789474
231 YSA 0.46729 0.772727
232 BT5 0.466102 0.845238
233 SMM 0.464646 0.72093
234 SAM 0.463918 0.72619
235 M24 0.46281 0.841463
236 YLY 0.46281 0.845238
237 A7D 0.462366 0.792208
238 A3D 0.462185 0.883117
239 NAE 0.459016 0.860759
240 7C5 0.458716 0.7875
241 SA8 0.458333 0.743902
242 8PZ 0.457944 0.793103
243 MHZ 0.457447 0.712644
244 71V 0.456522 0.85
245 A3G 0.455556 0.792208
246 B1U 0.453704 0.712766
247 SAI 0.453608 0.772152
248 SAH 0.453608 0.782051
249 6C6 0.453608 0.871795
250 PO4 PO4 A A A A PO4 0.451923 0.866667
251 NA7 0.451923 0.946667
252 Y3J 0.451219 0.697368
253 AVV 0.45098 0.910256
254 S7M 0.45 0.72619
255 7D7 0.45 0.736842
256 6IA 0.44898 0.807229
257 ENQ 0.447619 0.905405
258 J4G 0.447619 0.909091
259 WSA 0.447368 0.781609
260 D4F 0.447154 0.831325
261 NAJ PZO 0.446281 0.817073
262 FB0 0.446154 0.818182
263 EAD 0.444444 0.841463
264 6AD 0.444444 0.851852
265 AAT 0.444444 0.722892
266 K3K 0.444444 0.772152
267 EEM 0.444444 0.72619
268 NAQ 0.443548 0.839506
269 KOY 0.442478 0.794872
270 PGS 0.442105 0.82716
271 G2P 0.441176 0.898734
272 N0B 0.44 0.855422
273 ZID 0.44 0.883117
274 2SA 0.44 0.921053
275 AV2 0.44 0.857143
276 D5M 0.43956 0.868421
277 DA 0.43956 0.868421
278 NEC 0.43956 0.717949
279 CUU 0.4375 0.932432
280 4YB 0.4375 0.775281
281 QXP 0.436893 0.738636
282 GEK 0.436893 0.775
283 Z5A 0.436508 0.772727
284 V1N 0.436364 0.906667
285 K3E 0.436364 0.7625
286 V47 0.435644 0.776316
287 AAM 0.434783 0.905405
288 PLP AAD 0.434426 0.728261
289 GP2 0.434343 0.898734
290 3AT 0.434343 0.932432
291 NAJ PYZ 0.432 0.77907
292 AMZ 0.431818 0.855263
293 C2R 0.431818 0.868421
294 A3S 0.431579 0.802632
295 G1R 0.431373 0.873418
296 NO7 0.431373 0.871795
297 P1H 0.430769 0.821429
298 101 0.428571 0.844156
299 ARU 0.428571 0.807229
300 LQJ 0.427273 0.881579
301 GGZ 0.427184 0.795181
302 NWQ 0.426966 0.710526
303 6FA 0.425373 0.833333
304 A6D 0.424528 0.717647
305 QXG 0.424528 0.730337
306 NYZ 0.424242 0.898734
307 N5O 0.423913 0.75641
308 AIR 0.423529 0.84
309 6K6 0.423077 0.868421
310 DAT 0.42268 0.894737
311 A3T 0.42268 0.789474
312 649 0.422414 0.758242
313 NIA 0.422222 0.771084
314 R2V 0.420561 0.738636
315 DTP 0.42 0.894737
316 NDE 0.419847 0.871795
317 7RA 0.419355 0.893333
318 0UM 0.419048 0.73494
319 8Q2 0.418803 0.766667
320 FDA 0.41791 0.804598
321 FNK 0.417266 0.777778
322 SXZ 0.416667 0.746988
323 N6P 0.415094 0.853333
324 K2H 0.415094 0.728395
325 62X 0.415094 0.701149
326 8BR 0.414894 0.848101
327 N5A 0.414894 0.730769
328 NDC 0.413534 0.8625
329 KY2 0.413462 0.72619
330 3AD 0.411765 0.797297
331 K15 0.411215 0.717647
332 S8M 0.409524 0.775
333 SFD 0.408759 0.729167
334 FAD 0.408759 0.843373
335 FAS 0.408759 0.843373
336 K2K 0.407407 0.753086
337 KYB 0.40566 0.72619
338 KL2 0.404494 0.782051
339 AS 0.404255 0.825
340 K2R 0.40367 0.87013
341 QQY 0.402174 0.78481
342 ACK 0.402174 0.826667
343 7DD 0.402062 0.918919
344 K2W 0.401786 0.756098
345 NJP 0.401639 0.884615
346 TM1 0.4 0.747126
347 SLU 0.4 0.744444
348 KY5 0.4 0.740741
349 KB1 0.4 0.73494
350 EO7 0.4 0.761364
Similar Ligands (3D)
Ligand no: 1; Ligand: RBY; 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 : 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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