Ligand profile

RXV

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

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog PDB 2xcr UniProt Q99XG5 Formula C₂₅H₂₇N₅O₂S
Mol. weight 461.59 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RXV
PDB
2xcr
UniProt (similar protein)
Q99XG5
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 461.59 Da
LogP (Crippen) 3.75
H-bond donors 1
H-bond acceptors 8
TPSA 83.30 Ų
Rotatable bonds 7
Aromatic rings 3 / 5
Heavy atoms 33
Fraction sp³ C 0.40
Formula C₂₅H₂₇N₅O₂S

Drug-likeness

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

Permeability proxy High

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 83.3
  • −1 ≤ LogP ≤ 5 3.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 461.6
  • LogP ≤ 5 3.75
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 83.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(c1)c(c(cn2)C#N)CCN3CCC(CC3)NCc4cc5c(cn4)OCS5
InChI 
InChI=1S/C25H27N5O2S/c1-31-20-2-3-23-22(11-20)21(17(12-26)13-29-23)6-9-30-7-4-18(5-8-30)27-14-19-10-25-24(15-28-19)32-16-33-25/h2-3,10-11,13,15,18,27H,4-9,14,16H2,1H3
InChIKey 
NKXJSCXEAVZSMF-UHFFFAOYSA-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)