Ligand profile

SM8

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog PDB 2y3p UniProt P0AES5 Formula C₄₆H₄₂ClNO₁₈
Mol. weight 932.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SM8
PDB
2y3p
UniProt (similar protein)
P0AES5
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 932.28 Da
LogP (Crippen) 3.00
H-bond donors 8
H-bond acceptors 18
TPSA 309.42 Ų
Rotatable bonds 9
Aromatic rings 3 / 8
Heavy atoms 66
Fraction sp³ C 0.35
Formula C₄₆H₄₂ClNO₁₈

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 309.4
  • −1 ≤ LogP ≤ 5 3.00
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 932.3
  • LogP ≤ 5 3.00
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 309.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H]([C@@H](C[C@@H](O1)c2ccc3c(c2O)[C@@H]([C@@]45[C@H](C[C@@]6(CC(=CC(=O)[C@@]6([C@]4(C3=O)O5)O)C)O)O)O)OC(=O)\C=C\C=C\C=C\C=C\C(=O)NC7=C(c8ccc(c(c8OC7=O)Cl)O)O)OC(=O)C
InChI 
InChI=1S/C46H42ClNO18/c1-20-16-29(51)45(61)43(60,18-20)19-30(52)44-41(58)33-24(40(57)46(44,45)66-44)13-12-23(36(33)55)27-17-28(38(21(2)62-27)63-22(3)49)64-32(54)11-9-7-5-4-6-8-10-31(53)48-35-37(56)25-14-15-26(50)34(47)39(25)65-42(35)59/h4-16,21,27-28,30,38,41,50,52,55-56,58,60-61H,17-19H2,1-3H3,(H,48,53)/b6-4+,7-5+,10-8+,11-9+/t21-,27-,28-,30+,38-,41+,43-,44+,45-,46-/m1/s1
InChIKey 
PLEGMCYXNQPJNV-VHSVXIAXSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00521

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02784.

PDB 22

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 15

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)