Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS A:472;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
MG A:471;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
RDC A:501;
Valid;
none;
submit data
364.777 C18 H17 Cl O6 C[C@@...
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: RDC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 RDC 1 1
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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