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Receptor
PDB id Resolution Class Description Source Keywords
3KU0 1.9 Å EC: 3.2.2.22 STRUCTURE OF GAP31 WITH ADENINE AT ITS BINDING POCKET GELONIUM MULTIFLORUM PLANT SEEDS GLYCOSIDASE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: A NEW ACTIVITY OF ANTI-HIV AND ANTI-TUMOR PROTEIN GAP31: DNA ADENOSINE GLYCOSIDASE--STRUCTURAL AND MODELING INSIGHT INTO ITS FUNCTIONS. BIOCHEM.BIOPHYS.RES.COMMUN. V. 391 340 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADE A:800;
B:801;
Valid;
Valid;
none;
none;
submit data
135.127 C5 H5 N5 c1[nH...
NAG A:410;
B:411;
Part of Protein;
Part of Protein;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KU0 1.9 Å EC: 3.2.2.22 STRUCTURE OF GAP31 WITH ADENINE AT ITS BINDING POCKET GELONIUM MULTIFLORUM PLANT SEEDS GLYCOSIDASE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: A NEW ACTIVITY OF ANTI-HIV AND ANTI-TUMOR PROTEIN GAP31: DNA ADENOSINE GLYCOSIDASE--STRUCTURAL AND MODELING INSIGHT INTO ITS FUNCTIONS. BIOCHEM.BIOPHYS.RES.COMMUN. V. 391 340 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
23 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
24 2QET - ADE C5 H5 N5 c1[nH]c2c(....
25 1LPC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
26 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
27 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
29 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
30 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
32 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
33 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
34 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
35 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
36 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
37 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
38 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
39 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
40 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
41 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
43 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
44 1QCJ - APT C14 H13 N6 O3 c1cc(ccc1C....
45 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
46 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
47 5Z3J - NCA C6 H6 N2 O c1cc(cnc1)....
48 5Z3I - ADE C5 H5 N5 c1[nH]c2c(....
49 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
50 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
51 3HIT Ki = 6.4 nM DYN C30 H47 N10 O17 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADE; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 ADE 1 1
2 PM6 0.5 0.742857
3 ES4 0.463415 0.685714
4 6AP 0.428571 0.9375
5 XQG 0.422222 0.648649
6 M02 0.411765 0.630435
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KU0; Ligand: ADE; Similar sites found with APoc: 280
This union binding pocket(no: 1) in the query (biounit: 3ku0.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5WZU 7W3 None
2 5MFI LYS ARG LYS ARG LYS ARG LYS ARG None
3 5OWC AYZ None
4 5AEI LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG None
5 2ORV 4TA None
6 1N9L FMN None
7 3WUR O4B None
8 3T50 FMN None
9 4WUJ FMN None
10 1L6O SER LEU LYS LEU MET THR THR VAL None
11 1XXA ARG None
12 2C3Q GTX 0.809717
13 5T2U NAP 1.20968
14 1PZL MYR 1.26582
15 3FS1 MYR 1.30435
16 1T57 FMN 1.45631
17 2Z6C FMN 1.55039
18 1COY FAD 1.59363
19 1COY AND 1.59363
20 2FV5 541 1.59363
21 5BW4 SAM 1.59363
22 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 1.70068
23 1BKC INN 1.99203
24 1OKC CXT 1.99203
25 1N46 PFA 1.99203
26 2P1C GG3 1.99203
27 1M13 HYF 1.99203
28 1W4R TTP 2.05128
29 5FJN FAD 2.19298
30 5FJN BE2 2.19298
31 1UPF URF 2.23214
32 2EV1 OLA 2.25225
33 1XTT U5P 2.31481
34 1N1G BCP 2.39044
35 3LCV SAM 2.39044
36 5Y77 FAD 2.39044
37 4MOP 2H5 2.39044
38 1RYI GOA 2.39044
39 5X68 FAD 2.39044
40 4KVL PLM 2.39044
41 1RYI FAD 2.39044
42 2IVD FAD 2.39044
43 4HA6 FAD 2.39044
44 3KMZ EQO 2.39044
45 2JHP SAH 2.39044
46 2YG3 FAD 2.39044
47 2LBD REA 2.39044
48 5LX9 OLB 2.39044
49 2DPM SAM 2.39044
50 4ITU NAI 2.39044
51 3NB0 G6P 2.39044
52 4MRP GSH 2.39044
53 3O7B SAH 2.45902
54 3OVR 5SP 2.63158
55 2QJY SMA 2.6738
56 5ALC TIQ 2.77778
57 4E5N NAD 2.78884
58 4LY9 1YY 2.78884
59 1K0E TRP 2.78884
60 5HGR 45D 2.78884
61 5T67 JHZ 2.78884
62 5T67 SAH 2.78884
63 4ZCC FAD 2.78884
64 4MIX UD1 2.78884
65 2YB9 HA0 2.78884
66 1BRW URA 2.78884
67 1VQW FAD 2.78884
68 3RGA ILD 2.78884
69 4R38 RBF 2.85714
70 1YP1 LYS ASN LEU 2.9703
71 6G5J EM8 3.0303
72 2Z6D FMN 3.07692
73 2CHT TSA 3.14961
74 5JNN 6LM 3.15789
75 5DEY 59T 3.18725
76 3ICS FAD 3.18725
77 3ICT FAD 3.18725
78 3ICR FAD 3.18725
79 4YDD MGD 3.18725
80 4YDD MD1 3.18725
81 3GDN FAD 3.18725
82 4G2R H1L 3.18725
83 2C9E PID 3.18725
84 3QLM PLM 3.22581
85 4PGK Y69 3.27869
86 2GFD RDA 3.38983
87 2BVL GLC 3.58566
88 2BVL UDP 3.58566
89 5Z21 NAI 3.58566
90 1IN4 ADP 3.58566
91 1LVL NAD 3.58566
92 4PJT 2YQ 3.58566
93 1Q8A HCS 3.58566
94 4RW3 PLM 3.58566
95 5UGH 8AJ 3.58566
96 3AI3 SOE 3.58566
97 3BOF HCS 3.58566
98 5WRI A3P 3.58566
99 2FGE ALA ALA LEU THR ARG ALA 3.58566
100 5SVV FMN 3.64964
101 1R6N 434 3.79147
102 1C9K 5GP 3.88889
103 1OPK MYR 3.98406
104 3E1T FAD 3.98406
105 3CGD FAD 3.98406
106 3CGB FAD 3.98406
107 3CGD NAD 3.98406
108 3CGD COA 3.98406
109 5BUK FAD 3.98406
110 4GCZ FMN 3.98406
111 5NTW 98N 3.98406
112 5BRT FAD 3.98406
113 5I39 FAD 3.98406
114 4JNA FAD 3.98406
115 6A0S NDP 3.98406
116 6A0S HSE 3.98406
117 2A92 NAI 3.98406
118 1V25 ANP 3.98406
119 3LU1 UD2 3.98406
120 5NI5 8YB 3.98406
121 4CS4 ANP 4.0146
122 4CS4 AXZ 4.0146
123 1XZ3 ICF 4.02299
124 4C3Y ANB 4.38247
125 3QJ4 FAD 4.38247
126 2YPO PHE 4.38247
127 2GMH FAD 4.38247
128 4LA7 A1O 4.38247
129 6ANV MTT 4.38247
130 5WYF ILP 4.38247
131 3HST MLR 4.38247
132 5UQK U2F 4.38247
133 2ZKJ ADP 4.38247
134 2QX0 APC 4.40252
135 1YQZ FAD 4.78088
136 5EXT ADP 4.78088
137 2DBZ NAP 4.78088
138 3DWB RDF 4.78088
139 5WA0 MSS 4.78088
140 1Q3A NGH 4.84848
141 6GG9 FMN 4.93827
142 5CSD ACD 5.03145
143 1WG8 SAM 5.17928
144 5EEH P9P 5.17928
145 5EEH SAH 5.17928
146 1PZG A3D 5.17928
147 5AOV NAP 5.17928
148 6EOF ADP 5.17928
149 5EY0 GTP 5.17928
150 6ASY ATP 5.17928
151 5OJI ISN 5.17928
152 5OJI NAP 5.17928
153 1YP0 PEF 5.43933
154 4WKI 3PW 5.53191
155 1JNR FAD 5.57769
156 1H82 GZZ 5.57769
157 1H82 FAD 5.57769
158 5OD2 5ID 5.57769
159 5B0I BOG 5.57769
160 5FTB ANP 5.57769
161 4Q9M FPP 5.69106
162 4Q9M 2ZW 5.69106
163 3AB1 FAD 5.9761
164 4C9G CXT 5.9761
165 1Y8Q ATP 5.9761
166 2OYS FMN 6.19835
167 3E8T UQ8 6.36364
168 1R27 MGD 6.3745
169 4USQ FAD 6.3745
170 4D79 ATP 6.3745
171 1XVB BHL 6.3745
172 4RDI ATP 6.3745
173 4RDH AMP 6.3745
174 1JQ9 PHE LEU SER TYR LYS 6.61157
175 3FAL REA 6.61157
176 1RDT L79 6.61157
177 2UXI G50 6.66667
178 4XU6 TDA 6.66667
179 1V59 NAD 6.69456
180 1FFU FAD 6.74847
181 1REO FAD 6.77291
182 1NAA ABL 6.77291
183 1NAA 6FA 6.77291
184 3UCL FAD 6.77291
185 3UCL NAP 6.77291
186 3UCL CYH 6.77291
187 6ER9 FAD 6.77291
188 6ER9 NAP 6.77291
189 2WKQ FMN 6.77291
190 5ETR 5RW 6.8323
191 5ETR APC 6.8323
192 4POJ 2VP 6.92641
193 4OOE NDP 7.17131
194 4J7H TRH 7.17131
195 3KXC PLM 7.2165
196 5UWA 8ND 7.38916
197 1YOK P6L 7.56972
198 5K7K 6RJ 7.56972
199 1YUC EPH 7.56972
200 3JQM GTP 7.64331
201 1ZDU P3A 7.7551
202 5UNJ RJW 7.7551
203 5OC1 FAD 7.96813
204 5KOX FAD 7.96813
205 5KOX RFP 7.96813
206 4YSX FAD 7.96813
207 1RSG FAD 7.96813
208 4IKR PVP 7.96813
209 6BII NAP 8.10811
210 2B96 ANN 8.13008
211 1D4D FAD 8.36653
212 5IGI ZIT 8.36653
213 5IGI GMP 8.36653
214 3ZS7 ATP 8.36653
215 2Y31 SMQ 8.36653
216 1ATL 0QI 8.41584
217 2Z3Y F2N 8.76494
218 5IH1 6BQ 8.76494
219 5IH1 GDP 8.76494
220 4EIP FAD 8.76494
221 3EM1 TYD 8.90411
222 3IS2 FAD 9.09091
223 3CTY FAD 9.16335
224 5OSW AE4 9.16335
225 3P7N FMN 9.30233
226 5OCA 9QZ 9.52381
227 2BRY FAD 9.56175
228 4HEQ FMN 9.58904
229 3LZW FAD 9.96016
230 3LZW NAP 9.96016
231 4QJR PIZ 10.2041
232 3QXV MTX 10.3175
233 6GAS FAD 10.3586
234 3KLJ FAD 10.3586
235 2DKH FAD 10.3586
236 2VVM FAD 10.3586
237 2NPX NAD 10.3586
238 2NPX FAD 10.3586
239 1ZDT PEF 10.3734
240 1ZOY UQ1 10.6796
241 2JB2 PHE 10.757
242 2JB2 FAD 10.757
243 5TTJ FAD 11.1554
244 1T36 ADP 11.5538
245 2V0U FMN 11.6438
246 5EFW FMN 11.7241
247 5DJU FMN 11.7241
248 1KRP DT DT PST 11.9522
249 5VN0 FAD 11.9522
250 2VL8 UDP 11.9522
251 2VL8 CTS 11.9522
252 4GBD MCF 11.9522
253 3AD8 FAD 12.1212
254 3AD8 PYC 12.1212
255 2PR5 FMN 12.1212
256 4Q0A 4OA 12.3506
257 1I1Q TRP 12.3506
258 3JZB 4HY 12.749
259 2YVJ NAI 12.844
260 1R6U TYM 13.1474
261 1NU4 MLA 13.4021
262 2D5Z L35 13.4752
263 4IVG ANP 13.5458
264 4C2V YJA 13.6364
265 4EES FMN 14.7826
266 2C94 TSF 15
267 4II2 ATP 15.3374
268 2VVL FAD 15.9363
269 3FZG SAM 16.5
270 3OJI PYV 16.9312
271 5G3N X28 17.3228
272 2ZFZ ARG 18.9873
273 2GAG FAD 22.2222
274 2GAG FOA 22.2222
275 2GAG NAD 22.2222
276 4F07 FAD 23.1579
277 1TMM APC 24.6835
278 1TMM HHR 24.6835
279 1M48 FRG 30.0752
280 5DJT FMN 31.1475
Pocket No.: 2; Query (leader) PDB : 3KU0; Ligand: ADE; Similar sites found with APoc: 54
This union binding pocket(no: 2) in the query (biounit: 3ku0.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2GTE VA None
2 2GJ3 FAD None
3 3KB6 NAD 1.99203
4 3OKI OKI 2.14592
5 5X8G S0N 2.39044
6 4XYB NDP 2.39044
7 3FJO FMN 2.39044
8 4LY9 S6P 2.78884
9 4I4B 1CV 2.78884
10 2B4B COA 2.92398
11 2PO3 T4K 3.18725
12 3DHV DAL AMP 3.18725
13 3P0K FAD 3.18725
14 3K7M FAD 3.58566
15 6DVH FMN 3.58566
16 2RH1 CLR 3.58566
17 5F1V 3VN 3.58566
18 4NNB OAA 3.58566
19 1QAN SAH 4.09836
20 2FP2 TSA 4.21687
21 2GMH UQ5 4.38247
22 5IXK 6EW 4.38596
23 1ID0 ANP 4.60526
24 5TQZ GLC 4.66667
25 1RPN NDP 4.78088
26 1B8U NAD 4.78088
27 1YSL COA 5.17928
28 4YKG NAD 5.57769
29 4YKG FAD 5.57769
30 1P9P SAH 5.9761
31 5X62 SAH 5.9761
32 3GD4 FAD 6.3745
33 3OJF IMJ 6.3745
34 3OJF NDP 6.3745
35 1XKD NAP 6.3745
36 1FM9 9CR 6.72269
37 5K52 OCD 6.77291
38 4M8E 29V 6.92641
39 4D7E FAD 7.17131
40 1ZGA HMK 7.56972
41 4W6Z 8ID 7.96813
42 2JJK R15 8.36653
43 1OBV FMN 9.46746
44 6AIN FAD 9.56175
45 2IU8 PLM 9.96016
46 2DKH 3HB 10.3586
47 3G08 FEE 11.1111
48 3AD8 NAD 12.1212
49 3L9R L9R 12.2449
50 3CXH SMA 12.3077
51 4DS8 A8S 12.749
52 1PG4 PRX 18.3267
53 1PG4 COA 18.3267
54 2DYR PGV 28.5714
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