Receptor
PDB id Resolution Class Description Source Keywords
1Z5B 2 Å EC: 5.99.1.3 TOPOISOMERASE VI-B, ADP ALF4- BOUND DIMER FORM SULFOLOBUS SHIBATAE TOPOISOMERASE ARCHAEA ATPASE ISOMERASE
Ref.: STRUCTURAL DISSECTION OF ATP TURNOVER IN THE PROTOT GHL ATPASE TOPOVI. STRUCTURE V. 13 873 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALF ADP A:3001;
B:3002;
Valid;
Valid;
none;
none;
submit data
527.153 n/a [P+](...
MG A:2001;
B:2002;
B:2003;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:4001;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2HKJ 2 Å EC: 5.99.1.3 TOPOISOMERASE VI-B BOUND TO RADICICOL SULFOLOBUS SHIBATAE TOPOISOMERASE GHKL DRUG COMPLEX RADICICOL ISOMERASE
Ref.: STRUCTURAL BASIS FOR TOPOISOMERASE VI INHIBITION BY ANTI-HSP90 DRUG RADICICOL NUCLEIC ACIDS RES. V. 34 4269 2006
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1Z5B - ALF ADP n/a n/a
2 1Z59 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2HKJ - RDC C18 H17 Cl O6 C[C@@H]1C[....
4 1Z5A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1MX0 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 1Z5C - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1Z5B - ALF ADP n/a n/a
2 1Z59 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2HKJ - RDC C18 H17 Cl O6 C[C@@H]1C[....
4 1Z5A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1MX0 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 1Z5C - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1Z5B - ALF ADP n/a n/a
2 1Z59 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2HKJ - RDC C18 H17 Cl O6 C[C@@H]1C[....
4 1Z5A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1MX0 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
6 1Z5C - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALF ADP; Similar ligands found: 303
No: Ligand ECFP6 Tc MDL keys Tc
1 ADP ALF 1 1
2 ALF ADP 1 1
3 ADP PO3 0.8 0.918919
4 ATP MG 0.790123 0.907895
5 ADP MG 0.78481 0.907895
6 BEF ADP 0.775 0.934211
7 ADP BEF 0.775 0.934211
8 ADP VO4 0.752941 0.907895
9 VO4 ADP 0.752941 0.907895
10 ANP MG 0.712644 0.873418
11 AMP MG 0.708861 0.894737
12 AF3 ADP 3PG 0.707071 0.961039
13 ADP BMA 0.703297 0.871795
14 GAP 0.697674 0.871795
15 AMP 0.683544 0.868421
16 A 0.683544 0.868421
17 A2D 0.679012 0.87013
18 ADP 0.674699 0.87013
19 ATP A A A 0.666667 0.906667
20 BA3 0.662651 0.87013
21 ABM 0.658537 0.846154
22 AP5 0.654762 0.87013
23 B4P 0.654762 0.87013
24 AN2 0.647059 0.858974
25 AP2 0.642857 0.8375
26 A12 0.642857 0.8375
27 DAL AMP 0.641304 0.883117
28 AR6 AR6 0.64 0.894737
29 M33 0.639535 0.858974
30 SRA 0.634146 0.825
31 ACP 0.632184 0.848101
32 ATP 0.632184 0.87013
33 AHZ 0.627451 0.8
34 LA8 ALF 3PG 0.625 0.961039
35 AQP 0.625 0.87013
36 5FA 0.625 0.87013
37 APC 0.625 0.8375
38 AR6 0.625 0.87013
39 APR 0.625 0.87013
40 ALF ADP 3PG 0.625 0.961039
41 ADX 0.62069 0.788235
42 AU1 0.62069 0.848101
43 CA0 0.62069 0.848101
44 AGS 0.617977 0.82716
45 SAP 0.617977 0.82716
46 AD9 0.617977 0.871795
47 50T 0.613636 0.858974
48 MYR AMP 0.612245 0.8
49 ATF 0.608696 0.909091
50 A A 0.608247 0.87013
51 PRX 0.606742 0.825
52 ANP 0.604396 0.848101
53 TAT 0.604396 0.8375
54 ACQ 0.604396 0.848101
55 RBY 0.6 0.8375
56 ADV 0.6 0.8375
57 AMP DBH 0.588235 0.848101
58 4TA 0.585586 0.790698
59 5AL 0.580645 0.858974
60 TYR AMP 0.578431 0.860759
61 A1R 0.57732 0.817073
62 NAD IBO 0.576577 0.85
63 SON 0.573034 0.8375
64 MAP 0.572917 0.85
65 A22 0.572917 0.858974
66 AOC 0.569767 0.779221
67 SRP 0.568421 0.8375
68 5SV 0.56701 0.785714
69 ARG AMP 0.566038 0.790698
70 PO4 PO4 A A A A PO4 0.565657 0.88
71 GDP ALF 0.565657 0.9125
72 ADQ 0.561224 0.848101
73 NAJ PZO 0.556522 0.829268
74 Z5A 0.554622 0.764045
75 BIS 0.554455 0.886076
76 ADN 0.551282 0.776316
77 XYA 0.551282 0.776316
78 RAB 0.551282 0.776316
79 25A 0.55102 0.87013
80 OOB 0.55102 0.858974
81 8QN 0.55102 0.858974
82 OAD 0.55 0.848101
83 AFH 0.54717 0.864198
84 LPA AMP 0.546296 0.8
85 4AD 0.545455 0.85
86 AMO 0.545455 0.8375
87 PAJ 0.545455 0.797619
88 5AS 0.544444 0.725275
89 NAD 0.54386 0.883117
90 9SN 0.543689 0.875
91 DLL 0.54 0.858974
92 AHX 0.54 0.807229
93 00A 0.54 0.8625
94 1ZZ 0.539216 0.77907
95 3OD 0.539216 0.848101
96 JB6 0.539216 0.817073
97 TXA 0.539216 0.8375
98 NAJ PYZ 0.537815 0.853659
99 5N5 0.5375 0.753247
100 3UK 0.534653 0.848101
101 A3D 0.534483 0.871795
102 25L 0.533981 0.858974
103 A4D 0.530864 0.753247
104 5CD 0.530864 0.786667
105 LAD 0.529412 0.797619
106 WAQ 0.529412 0.817073
107 NAE 0.529412 0.85
108 PR8 0.529412 0.788235
109 NB8 0.524272 0.807229
110 PTJ 0.524272 0.807229
111 ME8 0.524272 0.77907
112 FYA 0.524272 0.835443
113 NAQ 0.512397 0.829268
114 EP4 0.511905 0.716049
115 G5A 0.510417 0.725275
116 YAP 0.509434 0.82716
117 FA5 0.509434 0.8375
118 G3A 0.509259 0.807229
119 AMP NAD 0.508197 0.860759
120 ZID 0.508197 0.871795
121 M2T 0.505882 0.719512
122 DTA 0.505882 0.746835
123 3DH 0.505747 0.734177
124 XAH 0.504673 0.77907
125 G5P 0.504587 0.807229
126 G A A A 0.504274 0.829268
127 GTA 0.5 0.8
128 4UV 0.5 0.82716
129 MTA 0.5 0.734177
130 NXX 0.5 0.860759
131 DND 0.5 0.860759
132 A3P 0.5 0.868421
133 NAI 0.5 0.817073
134 PAP 0.5 0.857143
135 OMR 0.495575 0.770115
136 TXE 0.495575 0.817073
137 TSB 0.49505 0.741573
138 A5A 0.494949 0.75
139 7D5 0.494253 0.7875
140 AP0 0.491228 0.807229
141 48N 0.491071 0.807229
142 7MD 0.490909 0.77907
143 4UU 0.490909 0.82716
144 SSA 0.49 0.725275
145 2A5 0.489583 0.802469
146 7D3 0.48913 0.790123
147 6RE 0.488889 0.722892
148 U A G G 0.487395 0.839506
149 NAX 0.486726 0.788235
150 6V0 0.486726 0.807229
151 UP5 0.486726 0.82716
152 TXD 0.486726 0.817073
153 TAD 0.486486 0.797619
154 VMS 0.485149 0.733333
155 54H 0.485149 0.733333
156 52H 0.485149 0.725275
157 ATR 0.484536 0.844156
158 NDE 0.484375 0.860759
159 A2P 0.483871 0.855263
160 3AM 0.483146 0.831169
161 TYM 0.482456 0.8375
162 LAQ 0.482143 0.77907
163 53H 0.480392 0.725275
164 5CA 0.480392 0.725275
165 N01 0.479339 0.883117
166 NMN AMP PO4 0.478992 0.85
167 T5A 0.478632 0.761364
168 139 0.478632 0.788235
169 4TC 0.478261 0.807229
170 J7C 0.478261 0.710843
171 A3N 0.478261 0.725
172 YLP 0.477876 0.761364
173 ZAS 0.477778 0.75
174 NDC 0.476923 0.829268
175 A A A 0.47619 0.883117
176 ALF 5GP 0.475248 0.9125
177 A4P 0.474138 0.744444
178 NAD BBN 0.474074 0.823529
179 4UW 0.473684 0.797619
180 GJV 0.473118 0.714286
181 S4M 0.473118 0.655556
182 P5A 0.471698 0.694737
183 ENQ 0.471698 0.868421
184 GSU 0.471698 0.725275
185 DSZ 0.471154 0.725275
186 NSS 0.471154 0.744444
187 LSS 0.471154 0.709677
188 7D4 0.46875 0.790123
189 MAO 0.468085 0.704545
190 DSH 0.467391 0.690476
191 NAD CJ3 0.467153 0.795455
192 COD 0.466667 0.736264
193 NVA LMS 0.466667 0.728261
194 ADJ 0.466102 0.770115
195 7MC 0.465517 0.761364
196 UPA 0.465517 0.817073
197 YLB 0.465517 0.761364
198 YLC 0.465517 0.77907
199 5X8 0.463918 0.725
200 IMO 0.462366 0.831169
201 LEU LMS 0.462264 0.728261
202 CNA 0.462185 0.860759
203 A U 0.461538 0.85
204 V3L 0.46 0.87013
205 KAA 0.457944 0.702128
206 IOT 0.457627 0.752809
207 A2R 0.456311 0.858974
208 2AM 0.455556 0.820513
209 PPS 0.455446 0.767442
210 DAL FAD PER 0.454545 0.772727
211 CNV FAD 0.453901 0.73913
212 YLA 0.453782 0.761364
213 ITT 0.453608 0.820513
214 5AD 0.451219 0.706667
215 AV2 0.45098 0.822785
216 FAD NBT 0.450704 0.701031
217 YSA 0.45045 0.725275
218 SAH 0.45 0.707317
219 AYB 0.45 0.752809
220 SFG 0.44898 0.7125
221 GDP AF3 0.448598 0.9125
222 FAD CNX 0.448276 0.68
223 M24 0.448 0.853659
224 4YB 0.447368 0.709677
225 Y3J 0.447059 0.756757
226 7D7 0.445783 0.705128
227 SAM 0.445545 0.678161
228 PAX 0.445312 0.770115
229 P33 FDA 0.445205 0.715789
230 P6G FDA 0.445205 0.73913
231 A7D 0.443299 0.7375
232 BTX 0.442623 0.761364
233 U G A 0.441176 0.8
234 6AD 0.441176 0.797619
235 OVE 0.44086 0.790123
236 SA8 0.44 0.674419
237 DZD 0.439024 0.797619
238 BT5 0.439024 0.752809
239 MHZ 0.438776 0.648352
240 NAD NDT 0.438356 0.714286
241 71V 0.4375 0.795181
242 A3G 0.43617 0.7375
243 6C6 0.435644 0.792683
244 SAI 0.435644 0.719512
245 DAT 0.434343 0.790123
246 GTP MG 0.433962 0.829268
247 SMM 0.432692 0.674157
248 WSA 0.432203 0.733333
249 7C5 0.429825 0.756098
250 NAD TDB 0.42953 0.666667
251 AAT 0.427184 0.674419
252 EEM 0.427184 0.697674
253 NAP 0.426357 0.871795
254 NAJ 0.42623 0.883117
255 A5D 0.425743 0.746835
256 YLY 0.425197 0.752809
257 PGS 0.424242 0.795181
258 GDP MG 0.423077 0.829268
259 TAP 0.423077 0.839506
260 NA7 0.422018 0.8375
261 DA 0.421053 0.7875
262 D5M 0.421053 0.7875
263 NEC 0.421053 0.6875
264 U A C C 0.420635 0.839506
265 AVV 0.420561 0.875
266 BEF GDP 0.420561 0.865854
267 GEK 0.420561 0.722892
268 649 0.420168 0.694737
269 EAD 0.419847 0.788235
270 NA0 0.419847 0.860759
271 NHD 0.419355 0.858974
272 NIA 0.419355 0.761905
273 GDP BEF 0.419048 0.853659
274 S7M 0.419048 0.678161
275 P1H 0.41791 0.770115
276 3AT 0.417476 0.846154
277 DTP 0.417476 0.790123
278 6IA 0.417476 0.755814
279 N0B 0.415385 0.761364
280 A3S 0.414141 0.746835
281 AMZ 0.413043 0.797468
282 C2R 0.413043 0.7875
283 FAD NBA 0.412903 0.686869
284 ARU 0.412844 0.797619
285 NFD 0.412698 0.910256
286 GGZ 0.411215 0.744186
287 101 0.410526 0.7875
288 2SA 0.409524 0.814815
289 A6D 0.409091 0.709302
290 U A A U 0.409091 0.839506
291 K15 0.409091 0.651685
292 6K6 0.407407 0.833333
293 A3T 0.405941 0.75641
294 AIR 0.404494 0.805195
295 0UM 0.40367 0.666667
296 6FA 0.402878 0.761364
297 AAM 0.402062 0.868421
298 ALF GDP 0.401869 0.897436
299 PLP AAD 0.401575 0.728261
300 FB0 0.40146 0.712766
301 7DD 0.4 0.857143
302 62X 0.4 0.637363
303 ACK 0.4 0.792208
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2HKJ; Ligand: RDC; Similar sites found: 52
This union binding pocket(no: 1) in the query (biounit: 2hkj.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.01373 0.43209 None
2 3TDC 0EU 0.02584 0.41867 1.27932
3 3CV2 COA 0.02161 0.42225 1.91898
4 1TV5 N8E 0.01839 0.43017 2.0316
5 1M2Z BOG 0.01712 0.43979 2.72374
6 1NF8 BOG 0.004633 0.46216 2.89855
7 3B9Z CO2 0.04689 0.42235 3.35052
8 5EOO CIT 0.02729 0.41101 3.77358
9 1XVB 3BR 0.002575 0.45408 4.70588
10 2VWA PTY 0.02877 0.41671 4.9505
11 4GCZ ADP 0.00001995 0.44342 5.45455
12 4MGA 27L 0.03602 0.41276 5.88235
13 3H4L ANP 0.000001292 0.49515 6.53951
14 1ID0 ANP 0.00001134 0.437 6.57895
15 1I58 ACP 0.0001949 0.42357 6.87831
16 1I58 ADP 0.0001018 0.40747 6.87831
17 3EHG ATP 0.003961 0.44014 7.03125
18 1XM4 PIL 0.02502 0.4008 7.78894
19 5V4R MGT 0.007216 0.44961 8.02469
20 1GKZ ADP 0.00001657 0.44972 8.76289
21 4URL XAM 0.00002421 0.49363 8.86699
22 4IPE ANP 0.000002918 0.53544 9.8081
23 4IVG ANP 0.000003863 0.49382 9.8081
24 5Y3N 8MF 0.00001506 0.56583 10.4478
25 1B63 ANP 0.0000105 0.52287 10.8108
26 2C2A ADP 0.0000001637 0.50283 10.8527
27 1Y8O ADP 0.0000005725 0.46105 11.2172
28 2ZKJ ADP 0.0000195 0.50503 11.4213
29 1BGQ RDC 0.000001354 0.52791 13.7778
30 1QY8 RDI 0.00000005416 0.51041 14.4981
31 3LE7 ADE 0.01473 0.42786 14.5594
32 2CB8 MYA 0.006127 0.44865 14.9425
33 3TL1 JRO 0.02191 0.41549 15.7233
34 5OCA 9QZ 0.001596 0.48021 15.873
35 4URN NOV 0.00008092 0.54374 16
36 2GFD RDA 0.0000003576 0.53001 16.5254
37 4XCL AGS 0.00000002764 0.54687 16.6023
38 5F5R ANP 0.00000001728 0.48525 16.8067
39 5IDM ANP 0.0000005963 0.48336 17.3184
40 1YC4 43P 0.00000001083 0.50904 17.4242
41 3D36 ADP 0.000001271 0.48256 17.623
42 3K60 ADP 0.0000007911 0.43374 17.9372
43 1S14 NOV 0.00005174 0.55396 18.0412
44 3NMQ 7PP 0.000008496 0.5633 19.2469
45 4B7P 9UN 0.0000002931 0.58773 20
46 2XCM ADP 0.000000171 0.6443 21.4953
47 1S16 ANP 0.00003875 0.49427 22.0513
48 2IOR ADP 0.00000005182 0.71176 22.9787
49 3A0T ADP 0.00005147 0.43245 27.6316
50 1TH8 ADP 0.00001426 0.41911 28.2759
51 2O1V ADP 0.00000001073 0.49783 28.5714
52 1TID ATP 0.00006698 0.42286 30.1471
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