Ligand profile

WCP

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

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog PDB 5bs3 UniProt P20831 Formula C₂₆H₂₆FN₅O₅
Mol. weight 507.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WCP
PDB
5bs3
UniProt (similar protein)
P20831
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 507.52 Da
LogP (Crippen) 1.72
H-bond donors 3
H-bond acceptors 9
TPSA 127.60 Ų
Rotatable bonds 5
Aromatic rings 3 / 8
Heavy atoms 37
Fraction sp³ C 0.46
Formula C₂₆H₂₆FN₅O₅

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 127.6
  • −1 ≤ LogP ≤ 5 1.72
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 507.5
  • LogP ≤ 5 1.72
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 127.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(nc1CNC34CCC(CC3)(OC4)C[C@@]5(CN6c7c5c(cnc7C=CC6=O)F)O)NC(=O)CO2
InChI 
InChI=1S/C26H26FN5O5/c27-16-10-28-17-2-4-20(34)32-13-26(35,21(16)22(17)32)12-25-7-5-24(6-8-25,14-37-25)29-9-15-1-3-18-23(30-15)31-19(33)11-36-18/h1-4,10,29,35H,5-9,11-14H2,(H,30,31,33)/t24?,25?,26-/m0/s1
InChIKey 
XTHQMKOHGLBSON-WNMGUVTHSA-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)