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Receptor
PDB id Resolution Class Description Source Keywords
1KHZ 2.04 Å EC: 3.6.1.13 STRUCTURE OF THE ADPR-ASE IN COMPLEX WITH AMPCPR AND MG ESCHERICHIA COLI NUDIX ADP-RIBOSE PYROPHOSPHATASE AMPCPR HYDROLASE
Ref.: MECHANISM OF THE ESCHERICHIA COLI ADP-RIBOSE PYROPHOSPHATASE, A NUDIX HYDROLASE. BIOCHEMISTRY V. 41 9279 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADV B:402;
Valid;
none;
submit data
557.343 C16 H25 N5 O13 P2 c1nc(...
CL A:401;
Invalid;
none;
submit data
35.453 Cl [Cl-]
MG B:301;
B:304;
B:310;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KHZ 2.04 Å EC: 3.6.1.13 STRUCTURE OF THE ADPR-ASE IN COMPLEX WITH AMPCPR AND MG ESCHERICHIA COLI NUDIX ADP-RIBOSE PYROPHOSPHATASE AMPCPR HYDROLASE
Ref.: MECHANISM OF THE ESCHERICHIA COLI ADP-RIBOSE PYROPHOSPHATASE, A NUDIX HYDROLASE. BIOCHEMISTRY V. 41 9279 2002
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1G9Q - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 1KHZ - ADV C16 H25 N5 O13 P2 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 5 families.
1 1G9Q - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 1KHZ - ADV C16 H25 N5 O13 P2 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 5 families.
1 1G9Q - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 1KHZ - ADV C16 H25 N5 O13 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADV; 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 : 1KHZ; Ligand: ADV; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 1khz.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1SS4 GSH None
2 2BOS GLA GAL GLC NBU None
3 1KJ1 MAN None
4 4IMO PWZ 1.13636
5 3GAC ENO 1.7094
6 2J5B TYE 1.91388
7 4LEB THR THR THR THR THR THR THR 1.91388
8 4OWK NGA 2.17391
9 6FA4 D1W 2.31214
10 2J83 BAT 2.39234
11 6GH9 MIX 2.87081
12 1OFZ FUL 2.87081
13 3U7Q HCA 2.87081
14 4LED XXR 2.87081
15 5J6Y GLC 3.19149
16 5J6Y BGC 3.19149
17 5LV1 78T 3.34928
18 5MZN ADP 3.34928
19 5JSP DQY 3.48259
20 4D52 GXL 3.82775
21 4D52 GIV 3.82775
22 5F7U GLC GLC 3.82775
23 6D61 4AA 4.10256
24 1J3R 6PG 4.21053
25 4YVN EBS 4.30622
26 1GPM AMP 4.30622
27 2JIG PD2 4.30622
28 4L77 CNL 4.30622
29 3MD0 GDP 4.30622
30 1GPM CIT 4.30622
31 3TK1 GDP 4.30622
32 4XDA RIB 4.30622
33 3GZ8 APR 4.32099
34 1ZS6 ADP 4.73373
35 1TZD ADP 4.78469
36 1QH8 HCA 4.78469
37 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 5.26316
38 1Y7P RIP 5.26316
39 4AF0 MOA 5.74163
40 1FDJ 13P 5.74163
41 3WG3 A2G GAL NAG FUC 6.17978
42 4JH6 FCN 6.52174
43 1EYQ NAR 6.69856
44 5AHW CMP 7.48299
45 4M1U A2G MBG 7.6555
46 5DEQ ARA 7.6555
47 1Q11 TYE 8.13397
48 1JT1 MCO 8.61244
49 5W6Y TRP 9.09091
50 4Y24 TD2 9.74026
51 5TPV TYD 10.0478
52 4J7H TLO 10.0478
53 1C3V PDC 10.5263
54 5GG9 8GT 11.0048
55 5ODQ 9SB 11.0048
56 5ISY NAD 11.4833
57 3A6T 8OG 11.6279
58 5GP0 GPP 14.094
59 3B6R CRN 14.3541
60 5ANU 58T 16.4557
61 1YKJ PHB 17.2249
62 2O1C PPV 17.3333
63 5BWD FUM 18.3333
64 1NFS DED 18.5792
65 1BHX ASP PHE GLU GLU ILE 22.449
66 6EHH 2GE 23.2955
67 1VHZ APR 31.3131
68 1SU2 ATP 33.9623
69 5C8L GLC 35.7143
70 2YVO AMP 36.2637
71 3O61 GDD 44.5026
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