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(=O)...
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: 307
No: Ligand ECFP6 Tc MDL keys Tc
1 ALF ADP 1 1
2 ADP ALF 1 1
3 ADP PO3 0.8 0.918919
4 ADP VO4 0.752941 0.907895
5 VO4 ADP 0.752941 0.907895
6 AF3 ADP 3PG 0.707071 0.961039
7 ADP BMA 0.703297 0.871795
8 GAP 0.697674 0.871795
9 AMP 0.683544 0.868421
10 A 0.683544 0.868421
11 A2D 0.679012 0.87013
12 ADP 0.674699 0.87013
13 ATP A A A 0.666667 0.906667
14 BA3 0.662651 0.87013
15 ABM 0.658537 0.846154
16 B4P 0.654762 0.87013
17 AP5 0.654762 0.87013
18 AT4 0.647059 0.8375
19 AN2 0.647059 0.858974
20 AP2 0.642857 0.8375
21 A12 0.642857 0.8375
22 DAL AMP 0.641304 0.883117
23 AR6 AR6 0.64 0.894737
24 M33 0.639535 0.858974
25 SRA 0.634146 0.825
26 HEJ 0.632184 0.87013
27 ACP 0.632184 0.848101
28 ATP 0.632184 0.87013
29 AHZ 0.627451 0.8
30 AQP 0.625 0.87013
31 APC 0.625 0.8375
32 APR 0.625 0.87013
33 5FA 0.625 0.87013
34 AR6 0.625 0.87013
35 ADX 0.62069 0.788235
36 CA0 0.62069 0.848101
37 AU1 0.62069 0.848101
38 AGS 0.617977 0.82716
39 AD9 0.617977 0.871795
40 SAP 0.617977 0.82716
41 50T 0.613636 0.858974
42 MYR AMP 0.612245 0.8
43 ATF 0.608696 0.909091
44 A A 0.608247 0.87013
45 PRX 0.606742 0.825
46 ANP 0.604396 0.848101
47 TAT 0.604396 0.8375
48 T99 0.604396 0.8375
49 ACQ 0.604396 0.848101
50 ADV 0.6 0.8375
51 RBY 0.6 0.8375
52 AMP DBH 0.588235 0.848101
53 4TA 0.585586 0.790698
54 6YZ 0.585106 0.848101
55 LMS 0.583333 0.767442
56 5AL 0.580645 0.858974
57 A1R 0.57732 0.817073
58 SON 0.573034 0.8375
59 MAP 0.572917 0.85
60 A22 0.572917 0.858974
61 TYR AMP 0.572816 0.85
62 AMP NAD 0.571429 0.883117
63 AOC 0.569767 0.779221
64 SRP 0.568421 0.8375
65 5SV 0.56701 0.785714
66 PO4 PO4 A A A A PO4 0.565657 0.88
67 ALF GDP 0.565657 0.9125
68 GDP ALF 0.565657 0.9125
69 9X8 0.565657 0.82716
70 ARG AMP 0.561905 0.790698
71 ADQ 0.561224 0.848101
72 A3R 0.561224 0.817073
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 RAB 0.551282 0.776316
78 XYA 0.551282 0.776316
79 OOB 0.55102 0.858974
80 25A 0.55102 0.87013
81 8QN 0.55102 0.858974
82 9ZD 0.55102 0.817073
83 9ZA 0.55102 0.817073
84 OAD 0.55 0.848101
85 AFH 0.54717 0.864198
86 LPA AMP 0.546296 0.8
87 PAJ 0.545455 0.797619
88 AMO 0.545455 0.8375
89 4AD 0.545455 0.85
90 5AS 0.544444 0.725275
91 NAD 0.54386 0.883117
92 9SN 0.543689 0.875
93 00A 0.54 0.8625
94 AHX 0.54 0.807229
95 DLL 0.54 0.858974
96 3OD 0.539216 0.848101
97 1ZZ 0.539216 0.77907
98 TXA 0.539216 0.8375
99 JB6 0.539216 0.817073
100 NAJ PYZ 0.537815 0.833333
101 5N5 0.5375 0.753247
102 3UK 0.534653 0.848101
103 A3D 0.534483 0.871795
104 25L 0.533981 0.858974
105 5CD 0.530864 0.786667
106 A4D 0.530864 0.753247
107 LAD 0.529412 0.797619
108 NAE 0.529412 0.85
109 PR8 0.529412 0.788235
110 WAQ 0.529412 0.817073
111 B5V 0.529412 0.8375
112 FYA 0.524272 0.835443
113 ME8 0.524272 0.77907
114 PTJ 0.524272 0.807229
115 NB8 0.524272 0.807229
116 NAQ 0.512397 0.829268
117 EP4 0.511905 0.716049
118 G5A 0.510417 0.725275
119 B5Y 0.509434 0.82716
120 B5M 0.509434 0.82716
121 YAP 0.509434 0.82716
122 FA5 0.509434 0.8375
123 G3A 0.509259 0.807229
124 ZID 0.508197 0.871795
125 DTA 0.505882 0.746835
126 M2T 0.505882 0.719512
127 3DH 0.505747 0.734177
128 XAH 0.504673 0.77907
129 GA7 0.504587 0.814815
130 G5P 0.504587 0.807229
131 G A A A 0.504274 0.829268
132 DQV 0.5 0.858974
133 GTA 0.5 0.8
134 MTA 0.5 0.734177
135 A3P 0.5 0.868421
136 4UV 0.5 0.82716
137 DND 0.5 0.860759
138 PAP 0.5 0.857143
139 NAI 0.5 0.817073
140 NXX 0.5 0.860759
141 OMR 0.495575 0.770115
142 TXE 0.495575 0.817073
143 TSB 0.49505 0.741573
144 A5A 0.494949 0.75
145 7D5 0.494253 0.7875
146 U A 0.491667 0.839506
147 A G 0.491525 0.839506
148 AP0 0.491228 0.807229
149 48N 0.491071 0.807229
150 7MD 0.490909 0.77907
151 4UU 0.490909 0.82716
152 SSA 0.49 0.725275
153 2A5 0.489583 0.802469
154 7D3 0.48913 0.790123
155 6RE 0.488889 0.722892
156 U A G G 0.487395 0.839506
157 UP5 0.486726 0.82716
158 NAX 0.486726 0.788235
159 TXD 0.486726 0.817073
160 6V0 0.486726 0.807229
161 TAD 0.486486 0.797619
162 54H 0.485149 0.733333
163 52H 0.485149 0.725275
164 VMS 0.485149 0.733333
165 ATR 0.484536 0.844156
166 NDE 0.484375 0.860759
167 A2P 0.483871 0.855263
168 3AM 0.483146 0.831169
169 TYM 0.482456 0.8375
170 LAQ 0.482143 0.77907
171 9K8 0.481132 0.758242
172 5CA 0.480392 0.725275
173 8X1 0.480392 0.702128
174 53H 0.480392 0.725275
175 N01 0.479339 0.883117
176 NMN AMP PO4 0.478992 0.85
177 139 0.478632 0.788235
178 T5A 0.478632 0.761364
179 4TC 0.478261 0.807229
180 J7C 0.478261 0.710843
181 A3N 0.478261 0.725
182 YLP 0.477876 0.761364
183 ZAS 0.477778 0.75
184 NDC 0.476923 0.829268
185 A A A 0.47619 0.883117
186 ALF 5GP 0.475248 0.9125
187 A4P 0.474138 0.744444
188 4UW 0.473684 0.797619
189 GJV 0.473118 0.714286
190 S4M 0.473118 0.655556
191 GSU 0.471698 0.725275
192 ENQ 0.471698 0.868421
193 P5A 0.471698 0.694737
194 DSZ 0.471154 0.725275
195 LSS 0.471154 0.709677
196 NSS 0.471154 0.744444
197 F2R 0.470588 0.761364
198 7D4 0.46875 0.790123
199 MAO 0.468085 0.704545
200 DSH 0.467391 0.690476
201 COD 0.466667 0.736264
202 NVA LMS 0.466667 0.72043
203 ADJ 0.466102 0.770115
204 UPA 0.465517 0.817073
205 YLB 0.465517 0.761364
206 YLC 0.465517 0.77907
207 7MC 0.465517 0.761364
208 5X8 0.463918 0.725
209 IMO 0.462366 0.831169
210 LEU LMS 0.462264 0.72043
211 CNA 0.462185 0.860759
212 A U 0.461538 0.85
213 V3L 0.46 0.87013
214 KAA 0.457944 0.702128
215 IOT 0.457627 0.752809
216 A2R 0.456311 0.858974
217 2AM 0.455556 0.820513
218 PPS 0.455446 0.767442
219 8PZ 0.454545 0.725275
220 CNV FAD 0.453901 0.764045
221 YLA 0.453782 0.761364
222 ITT 0.453608 0.820513
223 5AD 0.451219 0.706667
224 AV2 0.45098 0.822785
225 FAD NBT 0.450704 0.701031
226 YSA 0.45045 0.725275
227 SAH 0.45 0.707317
228 HFD 0.45 0.897436
229 AYB 0.45 0.752809
230 SFG 0.44898 0.7125
231 GDP AF3 0.448598 0.9125
232 FAD CNX 0.448276 0.68
233 M24 0.448 0.853659
234 4YB 0.447368 0.709677
235 80F 0.447154 0.761364
236 Y3J 0.447059 0.756757
237 7D7 0.445783 0.705128
238 SAM 0.445545 0.678161
239 PAX 0.445312 0.770115
240 P33 FDA 0.445205 0.715789
241 P6G FDA 0.445205 0.73913
242 A7D 0.443299 0.7375
243 BTX 0.442623 0.761364
244 6AD 0.441176 0.797619
245 OVE 0.44086 0.790123
246 SA8 0.44 0.674419
247 BT5 0.439024 0.752809
248 DZD 0.439024 0.797619
249 MHZ 0.438776 0.648352
250 71V 0.4375 0.795181
251 A3G 0.43617 0.7375
252 6C6 0.435644 0.792683
253 SAI 0.435644 0.719512
254 DAT 0.434343 0.790123
255 SMM 0.432692 0.674157
256 WSA 0.432203 0.733333
257 A C A C 0.432 0.829268
258 7C5 0.429825 0.756098
259 EEM 0.427184 0.697674
260 AAT 0.427184 0.674419
261 NAP 0.426357 0.871795
262 NAJ 0.42623 0.883117
263 A5D 0.425743 0.746835
264 YLY 0.425197 0.752809
265 PGS 0.424242 0.795181
266 TAP 0.423077 0.839506
267 NA7 0.422018 0.8375
268 D5M 0.421053 0.7875
269 DA 0.421053 0.7875
270 NEC 0.421053 0.6875
271 U A C C 0.420635 0.839506
272 GEK 0.420561 0.722892
273 AVV 0.420561 0.875
274 649 0.420168 0.694737
275 NA0 0.419847 0.860759
276 EAD 0.419847 0.788235
277 NHD 0.419355 0.858974
278 NIA 0.419355 0.761905
279 S7M 0.419048 0.678161
280 P1H 0.41791 0.770115
281 6IA 0.417476 0.755814
282 3AT 0.417476 0.846154
283 DTP 0.417476 0.790123
284 FAD NBA 0.415584 0.68
285 N0B 0.415385 0.761364
286 A3S 0.414141 0.746835
287 C2R 0.413043 0.7875
288 AMZ 0.413043 0.797468
289 ARU 0.412844 0.797619
290 NFD 0.412698 0.910256
291 GGZ 0.411215 0.744186
292 101 0.410526 0.7875
293 2SA 0.409524 0.814815
294 K15 0.409091 0.651685
295 U A A U 0.409091 0.839506
296 A6D 0.409091 0.709302
297 6K6 0.407407 0.833333
298 A3T 0.405941 0.75641
299 8Q2 0.404959 0.702128
300 AIR 0.404494 0.805195
301 0UM 0.40367 0.666667
302 6FA 0.402878 0.761364
303 AAM 0.402062 0.868421
304 FB0 0.40146 0.712766
305 7DD 0.4 0.857143
306 ACK 0.4 0.792208
307 62X 0.4 0.637363
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2HKJ; Ligand: RDC; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 2hkj.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5F5R ANP 16.8067
2 1YC4 43P 17.4242
3 2IOR ADP 22.9787
4 2O1V ADP 28.5714
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