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 27 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 25 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 21 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: 293
No: Ligand ECFP6 Tc MDL keys Tc
1 RBY 1 1
2 ADV 1 1
3 A12 0.810811 0.972973
4 AP2 0.810811 0.972973
5 AR6 0.805195 0.958904
6 APR 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 ABM 0.714286 0.881579
12 ACP 0.703704 0.959459
13 AMP MG 0.701299 0.857143
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 AN2 0.679012 0.92
22 PRX 0.674699 0.858974
23 ADX 0.670732 0.841463
24 CA0 0.670732 0.933333
25 AU1 0.670732 0.907895
26 50T 0.662651 0.894737
27 ATP 0.662651 0.932432
28 TAD 0.659794 0.923077
29 5FA 0.654762 0.932432
30 AQP 0.654762 0.932432
31 ADP MG 0.650602 0.87013
32 ADP PO3 0.647059 0.905405
33 AD9 0.647059 0.907895
34 SAP 0.647059 0.884615
35 AGS 0.647059 0.884615
36 ADP BEF 0.642857 0.848101
37 BEF ADP 0.642857 0.848101
38 ATP MG 0.639535 0.87013
39 ANP 0.632184 0.907895
40 TAT 0.632184 0.896104
41 GAP 0.632184 0.883117
42 5AL 0.625 0.92
43 SON 0.619048 0.946667
44 ATF 0.617977 0.896104
45 MAP 0.615385 0.884615
46 SRP 0.611111 0.921053
47 3OD 0.610526 0.933333
48 OAD 0.606383 0.933333
49 ADQ 0.602151 0.933333
50 4AD 0.602151 0.934211
51 ALF ADP 0.6 0.8375
52 ADP ALF 0.6 0.8375
53 DAL AMP 0.597826 0.894737
54 A22 0.597826 0.92
55 DLL 0.595745 0.92
56 ADP VO4 0.593407 0.894737
57 VO4 ADP 0.593407 0.894737
58 ANP MG 0.593407 0.860759
59 8QN 0.591398 0.92
60 5SV 0.591398 0.839506
61 OOB 0.591398 0.92
62 25A 0.591398 0.906667
63 A2R 0.586957 0.945946
64 PAJ 0.585106 0.875
65 A1R 0.585106 0.922078
66 AMO 0.585106 0.946667
67 XYA 0.581081 0.810811
68 RAB 0.581081 0.810811
69 ADN 0.581081 0.810811
70 00A 0.578947 0.873418
71 AHX 0.578947 0.886076
72 AOC 0.578313 0.789474
73 FYA 0.57732 0.894737
74 3UK 0.572917 0.907895
75 DZD 0.572727 0.923077
76 5AS 0.569767 0.752809
77 WAQ 0.56701 0.922078
78 LAD 0.56701 0.898734
79 PR8 0.56701 0.8875
80 5N5 0.565789 0.786667
81 NB8 0.561224 0.910256
82 BIS 0.561224 0.873418
83 1ZZ 0.561224 0.853659
84 ME8 0.561224 0.853659
85 PTJ 0.561224 0.8625
86 JB6 0.561224 0.873418
87 TXA 0.561224 0.921053
88 FA5 0.56 0.921053
89 5CD 0.558442 0.773333
90 A4D 0.558442 0.786667
91 ADP BMA 0.556701 0.907895
92 MYR AMP 0.555556 0.831325
93 25L 0.555556 0.92
94 A A 0.55102 0.881579
95 9SN 0.55 0.8625
96 M2T 0.55 0.707317
97 G5A 0.549451 0.772727
98 YAP 0.544554 0.909091
99 ATP A A A 0.544554 0.893333
100 A3P 0.54023 0.905405
101 TYR AMP 0.539216 0.871795
102 XAH 0.539216 0.853659
103 AFH 0.538462 0.898734
104 EP4 0.5375 0.725
105 4TC 0.537037 0.910256
106 7D5 0.536585 0.844156
107 4UV 0.533981 0.884615
108 AMP DBH 0.533981 0.883117
109 DTA 0.530864 0.779221
110 3DH 0.53012 0.74359
111 G3A 0.528846 0.8625
112 AHZ 0.528302 0.809524
113 LAQ 0.528302 0.853659
114 OMR 0.527778 0.865854
115 MTA 0.52439 0.74359
116 4UU 0.52381 0.884615
117 G5P 0.52381 0.8625
118 3AM 0.52381 0.866667
119 LPA AMP 0.523364 0.831325
120 A2P 0.522727 0.891892
121 GTA 0.518868 0.831325
122 TXD 0.518519 0.873418
123 NAX 0.518519 0.864198
124 4UW 0.518519 0.851852
125 UP5 0.518519 0.884615
126 A5A 0.515789 0.77907
127 TSB 0.515464 0.790698
128 ARG AMP 0.514019 0.821429
129 TYM 0.513761 0.921053
130 6RE 0.511628 0.731707
131 S4M 0.511364 0.681818
132 SSA 0.510417 0.793103
133 AR6 AR6 0.509434 0.906667
134 7MD 0.509434 0.876543
135 48N 0.509259 0.910256
136 YLP 0.509259 0.855422
137 AP0 0.509091 0.8625
138 PAP 0.505376 0.918919
139 VMS 0.505155 0.761364
140 54H 0.505155 0.761364
141 52H 0.505155 0.752809
142 DND 0.504587 0.921053
143 NXX 0.504587 0.921053
144 6V0 0.504587 0.8625
145 NAI 0.504587 0.873418
146 53H 0.5 0.752809
147 TXE 0.5 0.873418
148 5CA 0.5 0.793103
149 J7C 0.5 0.740741
150 ZAS 0.5 0.7375
151 IMO 0.5 0.866667
152 A3N 0.5 0.75641
153 YLC 0.495495 0.876543
154 UPA 0.495495 0.873418
155 YLB 0.495495 0.855422
156 V3L 0.494737 0.932432
157 2A5 0.494624 0.883117
158 7D3 0.494382 0.87013
159 2AM 0.494118 0.88
160 AYB 0.491228 0.845238
161 A4P 0.491071 0.793103
162 P5A 0.490196 0.758242
163 DSZ 0.49 0.813953
164 NSS 0.49 0.793103
165 LSS 0.49 0.755556
166 PPS 0.489583 0.819277
167 ATR 0.489362 0.905405
168 7D4 0.48913 0.87013
169 MAO 0.488889 0.77381
170 DSH 0.488636 0.740741
171 IOT 0.486726 0.845238
172 AF3 ADP 3PG 0.486486 0.851852
173 LA8 ALF 3PG 0.486486 0.851852
174 ALF ADP 3PG 0.486486 0.851852
175 NVA LMS 0.485149 0.736264
176 5X8 0.483871 0.779221
177 T5A 0.482456 0.855422
178 YLA 0.482456 0.855422
179 139 0.482456 0.864198
180 ADJ 0.482456 0.865854
181 7MC 0.482143 0.855422
182 LEU LMS 0.480392 0.736264
183 CNA 0.478261 0.896104
184 GJV 0.477778 0.722892
185 OVE 0.477273 0.846154
186 GSU 0.475728 0.793103
187 KAA 0.475728 0.766667
188 5AD 0.474359 0.716216
189 A5D 0.473684 0.779221
190 ITT 0.473118 0.88
191 4TA 0.470085 0.821429
192 COD 0.470085 0.825581
193 NAD 0.470085 0.894737
194 BTX 0.470085 0.833333
195 SFG 0.468085 0.789474
196 YSA 0.46729 0.772727
197 BT5 0.466102 0.845238
198 SMM 0.464646 0.72093
199 SAM 0.463918 0.72619
200 YLY 0.46281 0.845238
201 M24 0.46281 0.841463
202 A7D 0.462366 0.792208
203 A3D 0.462185 0.883117
204 NAD IBO 0.461538 0.8375
205 NAE 0.459016 0.860759
206 7C5 0.458716 0.7875
207 SA8 0.458333 0.743902
208 G A A A 0.457627 0.817073
209 MHZ 0.457447 0.712644
210 71V 0.456522 0.85
211 A3G 0.455556 0.792208
212 SAH 0.453608 0.782051
213 6C6 0.453608 0.871795
214 SAI 0.453608 0.772152
215 A A A 0.451923 0.92
216 PO4 PO4 A A A A PO4 0.451923 0.866667
217 NA7 0.451923 0.946667
218 Y3J 0.451219 0.697368
219 AVV 0.45098 0.910256
220 S7M 0.45 0.72619
221 7D7 0.45 0.736842
222 6IA 0.44898 0.807229
223 ENQ 0.447619 0.905405
224 WSA 0.447368 0.781609
225 NAJ PZO 0.446281 0.817073
226 FB0 0.446154 0.818182
227 6AD 0.444444 0.851852
228 EAD 0.444444 0.841463
229 EEM 0.444444 0.72619
230 AAT 0.444444 0.722892
231 NAJ PYZ 0.443548 0.819277
232 NAQ 0.443548 0.839506
233 PGS 0.442105 0.82716
234 U A G G 0.441667 0.82716
235 G2P 0.441176 0.898734
236 AV2 0.44 0.857143
237 ZID 0.44 0.883117
238 AMP NAD 0.44 0.871795
239 N0B 0.44 0.855422
240 2SA 0.44 0.921053
241 D5M 0.43956 0.868421
242 NEC 0.43956 0.717949
243 DA 0.43956 0.868421
244 4YB 0.4375 0.775281
245 GEK 0.436893 0.775
246 Z5A 0.436508 0.772727
247 V1N 0.436364 0.906667
248 AAM 0.434783 0.905405
249 GP2 0.434343 0.898734
250 3AT 0.434343 0.932432
251 AMZ 0.431818 0.855263
252 C2R 0.431818 0.868421
253 A3S 0.431579 0.802632
254 G1R 0.431373 0.873418
255 P1H 0.430769 0.821429
256 101 0.428571 0.844156
257 ARU 0.428571 0.807229
258 A U 0.42735 0.8375
259 GGZ 0.427184 0.795181
260 PLP AAD 0.42623 0.736264
261 6FA 0.425373 0.833333
262 A6D 0.424528 0.717647
263 AIR 0.423529 0.84
264 6K6 0.423077 0.868421
265 A3T 0.42268 0.789474
266 DAT 0.42268 0.894737
267 649 0.422414 0.758242
268 NIA 0.422222 0.771084
269 DTP 0.42 0.894737
270 NDE 0.419847 0.871795
271 7RA 0.419355 0.893333
272 0UM 0.419048 0.73494
273 FDA 0.41791 0.804598
274 FNK 0.417266 0.777778
275 SXZ 0.416667 0.746988
276 N6P 0.415094 0.853333
277 62X 0.415094 0.701149
278 8BR 0.414894 0.848101
279 NDC 0.413534 0.8625
280 3AD 0.411765 0.797297
281 K15 0.411215 0.717647
282 S8M 0.409524 0.775
283 FAS 0.408759 0.843373
284 FAD 0.408759 0.843373
285 SFD 0.408759 0.729167
286 AS 0.404255 0.825
287 QQY 0.402174 0.78481
288 ACK 0.402174 0.826667
289 7DD 0.402062 0.918919
290 NJP 0.401639 0.884615
291 TM1 0.4 0.747126
292 KB1 0.4 0.73494
293 SLU 0.4 0.744444
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YVO; Ligand: AMP; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 2yvo.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BTN I3P 0.0103 0.46295 None
2 1UO5 PIH 0.02679 0.42935 None
3 2BOS GLA GAL 0.005563 0.42622 None
4 1ZJ6 G3D 0.001896 0.42106 None
5 2WGC SIA GAL BGC 0.03836 0.42055 None
6 3S9K CIT 0.03282 0.41856 None
7 2BOS GLA GAL GLC 0.007764 0.40961 None
8 3MAG 3MA 0.006225 0.45522 1.0989
9 1W3R PYR 0.003565 0.45103 2.74725
10 5LKC FUC GLA A2G 0.03395 0.42886 2.74725
11 3BHO B4P 0.02988 0.41888 2.74725
12 3QDT A2G GAL 0.009129 0.43112 2.7972
13 3JQ3 ADP 0.001513 0.42988 3.2967
14 3F81 STT 0.02167 0.41917 3.84615
15 1UF5 CDT 0.006117 0.40586 3.84615
16 2Z9V PXM 0.01115 0.40442 3.84615
17 4F8L GAL 0.008258 0.45795 4.13793
18 1TUV VK3 0.009911 0.43651 4.38596
19 1H0C AOA 0.003581 0.44366 4.3956
20 4PPU TYR 0.008265 0.40992 4.3956
21 2EB5 OXL 0.0008884 0.46435 4.86891
22 1SS4 GSH 0.005417 0.47231 4.94506
23 1SS4 CIT 0.009834 0.44108 4.94506
24 2B7N NTM 0.006198 0.42052 4.94506
25 1GJW GLC 0.02319 0.40552 4.94506
26 1YOA FMN 0.002892 0.4833 5.03145
27 4RJK PYR 0.004678 0.44528 5.49451
28 1WDA BAG 0.002675 0.42517 5.49451
29 2F2U M77 0.004225 0.41223 5.49451
30 1TDF NAP 0.01133 0.40873 5.49451
31 3P3N AKG 0.0235 0.40525 5.49451
32 1TDF FAD 0.005961 0.40433 5.49451
33 2Y0I AKG 0.02743 0.40431 5.49451
34 3R51 MMA 0.002514 0.46677 6.04396
35 2V5E SCR 0.01013 0.44399 6.04396
36 4M5P MLA 0.02104 0.42705 6.04396
37 1RZM E4P 0.00974 0.42327 6.04396
38 4M5P 23W 0.02578 0.40902 6.04396
39 2ZWS PLM 0.01081 0.45143 6.59341
40 4JH6 FCN 0.009785 0.42195 8.79121
41 1XE7 GUN 0.02356 0.41731 9.34066
42 1T0S BML 0.01468 0.42103 11.5385
43 1MZV AMP 0.002934 0.4185 11.5385
44 1QVJ RP5 0.008456 0.43356 12.0879
45 1HFU NAG NDG 0.00811 0.42213 12.6374
46 3GZ8 APR 0.002139 0.41253 13.5802
47 4F4S EFO 0.01061 0.40534 14.4737
48 2GPT TLA 0.01956 0.4125 15.9341
49 1KHZ ADV 0.00002629 0.48012 36.2637
50 1MK1 APR 0.000005202 0.52473 37.3626
51 3ACA 8DD 0.0008108 0.42942 41.7582
Feedback