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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 24 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: 307
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 APC 0.805195 0.972973
6 AR6 0.805195 0.958904
7 APR 0.805195 0.958904
8 A 0.743243 0.905405
9 AMP 0.743243 0.905405
10 ABM 0.714286 0.881579
11 A2D 0.714286 0.932432
12 ACP 0.703704 0.959459
13 BA3 0.696203 0.932432
14 M33 0.691358 0.92
15 ACQ 0.690476 0.959459
16 SRA 0.688312 0.858974
17 B4P 0.6875 0.932432
18 ADP 0.6875 0.932432
19 AP5 0.6875 0.932432
20 AN2 0.679012 0.92
21 AT4 0.679012 0.896104
22 PRX 0.674699 0.858974
23 CA0 0.670732 0.933333
24 ADX 0.670732 0.841463
25 AU1 0.670732 0.907895
26 6YZ 0.666667 0.959459
27 50T 0.662651 0.894737
28 ATP 0.662651 0.932432
29 HEJ 0.662651 0.932432
30 TAD 0.659794 0.923077
31 AQP 0.654762 0.932432
32 5FA 0.654762 0.932432
33 ADP PO3 0.647059 0.905405
34 AD9 0.647059 0.907895
35 SAP 0.647059 0.884615
36 AGS 0.647059 0.884615
37 GAP 0.632184 0.883117
38 T99 0.632184 0.896104
39 TAT 0.632184 0.896104
40 ANP 0.632184 0.907895
41 5AL 0.625 0.92
42 SON 0.619048 0.946667
43 ATF 0.617977 0.896104
44 MAP 0.615385 0.884615
45 LMS 0.6125 0.797619
46 SRP 0.611111 0.921053
47 3OD 0.610526 0.933333
48 9ZD 0.608696 0.873418
49 9ZA 0.608696 0.873418
50 9X8 0.606383 0.909091
51 OAD 0.606383 0.933333
52 4AD 0.602151 0.934211
53 ADQ 0.602151 0.933333
54 ALF ADP 0.6 0.8375
55 ADP ALF 0.6 0.8375
56 DAL AMP 0.597826 0.894737
57 A22 0.597826 0.92
58 DLL 0.595745 0.92
59 ADP VO4 0.593407 0.894737
60 VO4 ADP 0.593407 0.894737
61 25A 0.591398 0.906667
62 OOB 0.591398 0.92
63 8QN 0.591398 0.92
64 5SV 0.591398 0.839506
65 A2R 0.586957 0.945946
66 A3R 0.585106 0.922078
67 A1R 0.585106 0.922078
68 PAJ 0.585106 0.875
69 AMO 0.585106 0.946667
70 B5V 0.583333 0.896104
71 ADN 0.581081 0.810811
72 XYA 0.581081 0.810811
73 RAB 0.581081 0.810811
74 00A 0.578947 0.873418
75 AHX 0.578947 0.886076
76 AOC 0.578313 0.789474
77 FYA 0.57732 0.894737
78 3UK 0.572917 0.907895
79 DZD 0.572727 0.923077
80 5AS 0.569767 0.752809
81 LAD 0.56701 0.898734
82 WAQ 0.56701 0.922078
83 PR8 0.56701 0.8875
84 5N5 0.565789 0.786667
85 NB8 0.561224 0.910256
86 PTJ 0.561224 0.8625
87 1ZZ 0.561224 0.853659
88 TXA 0.561224 0.921053
89 BIS 0.561224 0.873418
90 JB6 0.561224 0.873418
91 ME8 0.561224 0.853659
92 B5Y 0.56 0.884615
93 FA5 0.56 0.921053
94 5CD 0.558442 0.773333
95 A4D 0.558442 0.786667
96 ADP BMA 0.556701 0.907895
97 25L 0.555556 0.92
98 MYR AMP 0.555556 0.831325
99 A A 0.55102 0.881579
100 M2T 0.55 0.707317
101 9SN 0.55 0.8625
102 G5A 0.549451 0.772727
103 ATP A A A 0.544554 0.893333
104 YAP 0.544554 0.909091
105 B5M 0.544554 0.884615
106 A3P 0.54023 0.905405
107 XAH 0.539216 0.853659
108 GA7 0.538462 0.896104
109 AFH 0.538462 0.898734
110 EP4 0.5375 0.725
111 4TC 0.537037 0.910256
112 7D5 0.536585 0.844156
113 4UV 0.533981 0.884615
114 AMP DBH 0.533981 0.883117
115 TYR AMP 0.533981 0.884615
116 DQV 0.533333 0.92
117 DTA 0.530864 0.779221
118 3DH 0.53012 0.74359
119 G3A 0.528846 0.8625
120 AHZ 0.528302 0.809524
121 LAQ 0.528302 0.853659
122 OMR 0.527778 0.865854
123 MTA 0.52439 0.74359
124 ARG AMP 0.52381 0.821429
125 4UU 0.52381 0.884615
126 G5P 0.52381 0.8625
127 3AM 0.52381 0.866667
128 LPA AMP 0.523364 0.831325
129 A2P 0.522727 0.891892
130 GTA 0.518868 0.831325
131 4UW 0.518519 0.851852
132 NAX 0.518519 0.864198
133 TXD 0.518519 0.873418
134 UP5 0.518519 0.884615
135 A5A 0.515789 0.77907
136 TSB 0.515464 0.790698
137 TYM 0.513761 0.921053
138 6RE 0.511628 0.731707
139 S4M 0.511364 0.681818
140 SSA 0.510417 0.793103
141 AR6 AR6 0.509434 0.906667
142 7MD 0.509434 0.876543
143 48N 0.509259 0.910256
144 YLP 0.509259 0.855422
145 AP0 0.509091 0.8625
146 PAP 0.505376 0.918919
147 54H 0.505155 0.761364
148 52H 0.505155 0.752809
149 VMS 0.505155 0.761364
150 DND 0.504587 0.921053
151 NAI 0.504587 0.873418
152 NXX 0.504587 0.921053
153 6V0 0.504587 0.8625
154 J7C 0.5 0.740741
155 5CA 0.5 0.793103
156 A3N 0.5 0.75641
157 8X1 0.5 0.747253
158 53H 0.5 0.752809
159 TXE 0.5 0.873418
160 IMO 0.5 0.866667
161 9K8 0.5 0.709677
162 ZAS 0.5 0.7375
163 YLB 0.495495 0.855422
164 UPA 0.495495 0.873418
165 YLC 0.495495 0.876543
166 V3L 0.494737 0.932432
167 2A5 0.494624 0.883117
168 7D3 0.494382 0.87013
169 2AM 0.494118 0.88
170 AYB 0.491228 0.845238
171 A4P 0.491071 0.793103
172 P5A 0.490196 0.758242
173 NSS 0.49 0.793103
174 DSZ 0.49 0.813953
175 LSS 0.49 0.755556
176 PPS 0.489583 0.819277
177 ATR 0.489362 0.905405
178 7D4 0.48913 0.87013
179 MAO 0.488889 0.77381
180 DSH 0.488636 0.740741
181 IOT 0.486726 0.845238
182 AF3 ADP 3PG 0.486486 0.851852
183 NVA LMS 0.485149 0.747253
184 5X8 0.483871 0.779221
185 ADJ 0.482456 0.865854
186 T5A 0.482456 0.855422
187 139 0.482456 0.864198
188 YLA 0.482456 0.855422
189 7MC 0.482143 0.855422
190 LEU LMS 0.480392 0.747253
191 CNA 0.478261 0.896104
192 GJV 0.477778 0.722892
193 OVE 0.477273 0.846154
194 KAA 0.475728 0.766667
195 GSU 0.475728 0.793103
196 80F 0.474576 0.855422
197 5AD 0.474359 0.716216
198 F2R 0.474138 0.855422
199 A5D 0.473684 0.779221
200 ITT 0.473118 0.88
201 4TA 0.470085 0.821429
202 AMP NAD 0.470085 0.894737
203 BTX 0.470085 0.833333
204 NAD 0.470085 0.894737
205 COD 0.470085 0.825581
206 HFD 0.46875 0.884615
207 SFG 0.468085 0.789474
208 YSA 0.46729 0.772727
209 BT5 0.466102 0.845238
210 SMM 0.464646 0.72093
211 SAM 0.463918 0.72619
212 YLY 0.46281 0.845238
213 M24 0.46281 0.841463
214 A7D 0.462366 0.792208
215 A3D 0.462185 0.883117
216 NAE 0.459016 0.860759
217 7C5 0.458716 0.7875
218 SA8 0.458333 0.743902
219 8PZ 0.457944 0.793103
220 G A A A 0.457627 0.817073
221 MHZ 0.457447 0.712644
222 71V 0.456522 0.85
223 A3G 0.455556 0.792208
224 SAH 0.453608 0.782051
225 SAI 0.453608 0.772152
226 6C6 0.453608 0.871795
227 PO4 PO4 A A A A PO4 0.451923 0.866667
228 A A A 0.451923 0.92
229 NA7 0.451923 0.946667
230 Y3J 0.451219 0.697368
231 AVV 0.45098 0.910256
232 7D7 0.45 0.736842
233 S7M 0.45 0.72619
234 6IA 0.44898 0.807229
235 ENQ 0.447619 0.905405
236 WSA 0.447368 0.781609
237 U A 0.446281 0.85
238 NAJ PZO 0.446281 0.817073
239 FB0 0.446154 0.818182
240 A G 0.445378 0.82716
241 EAD 0.444444 0.841463
242 AAT 0.444444 0.722892
243 6AD 0.444444 0.851852
244 EEM 0.444444 0.72619
245 NAQ 0.443548 0.839506
246 PGS 0.442105 0.82716
247 U A G G 0.441667 0.82716
248 G2P 0.441176 0.898734
249 AV2 0.44 0.857143
250 N0B 0.44 0.855422
251 2SA 0.44 0.921053
252 ZID 0.44 0.883117
253 D5M 0.43956 0.868421
254 DA 0.43956 0.868421
255 NEC 0.43956 0.717949
256 4YB 0.4375 0.775281
257 GEK 0.436893 0.775
258 Z5A 0.436508 0.772727
259 V1N 0.436364 0.906667
260 AAM 0.434783 0.905405
261 GP2 0.434343 0.898734
262 3AT 0.434343 0.932432
263 NAJ PYZ 0.432 0.77907
264 AMZ 0.431818 0.855263
265 C2R 0.431818 0.868421
266 A3S 0.431579 0.802632
267 G1R 0.431373 0.873418
268 P1H 0.430769 0.821429
269 101 0.428571 0.844156
270 ARU 0.428571 0.807229
271 A U 0.42735 0.8375
272 GGZ 0.427184 0.795181
273 6FA 0.425373 0.833333
274 A6D 0.424528 0.717647
275 AIR 0.423529 0.84
276 6K6 0.423077 0.868421
277 DAT 0.42268 0.894737
278 A3T 0.42268 0.789474
279 649 0.422414 0.758242
280 NIA 0.422222 0.771084
281 DTP 0.42 0.894737
282 NDE 0.419847 0.871795
283 7RA 0.419355 0.893333
284 0UM 0.419048 0.73494
285 8Q2 0.418803 0.766667
286 FDA 0.41791 0.804598
287 FNK 0.417266 0.777778
288 SXZ 0.416667 0.746988
289 62X 0.415094 0.701149
290 N6P 0.415094 0.853333
291 8BR 0.414894 0.848101
292 NDC 0.413534 0.8625
293 3AD 0.411765 0.797297
294 K15 0.411215 0.717647
295 S8M 0.409524 0.775
296 FAS 0.408759 0.843373
297 SFD 0.408759 0.729167
298 FAD 0.408759 0.843373
299 AS 0.404255 0.825
300 ACK 0.402174 0.826667
301 QQY 0.402174 0.78481
302 7DD 0.402062 0.918919
303 NJP 0.401639 0.884615
304 KB1 0.4 0.73494
305 EO7 0.4 0.761364
306 SLU 0.4 0.744444
307 TM1 0.4 0.747126
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: 29
This union binding pocket(no: 1) in the query (biounit: 2yvo.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL None
2 2BOS GLA GAL GLC None
3 4M1U A2G MBG 1.0989
4 4KYS VIB 2.74725
5 2P7Q GG6 3.00752
6 2P39 SCR 3.22581
7 2ICK DMA 3.2967
8 4A3X LAT 4.3956
9 5EOO CIT 4.3956
10 3P3N AKG 5.49451
11 2XUM OGA 5.49451
12 2Y0I AKG 5.49451
13 4JH6 FCN 8.79121
14 5GG9 8GT 10.4396
15 6EHH 2GE 10.7955
16 5HZX 2GE 10.7955
17 1QVJ RP5 12.0879
18 1HFU NAG NDG 12.6374
19 3GZ8 APR 13.5802
20 2GPT TLA 15.9341
21 2QJT AMP 17.033
22 1NFS DED 18.1319
23 5GP0 GPP 25.2747
24 5ISY NAD 27.4725
25 3X0K AR6 33.5165
26 1KHZ ADV 36.2637
27 1MK1 APR 37.3626
28 5NQR 958 41.7582
29 5C8L GLC 47.8022
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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