Ligand profile

ZINC9210767

Virtual-screening candidate from ZINC.

Bound to: VK055_4925 — apurinic endonuclease family protein

Via homolog UniProt P0A6C1 Formula C₂₁H₂₈N₆O₄
Tanimoto 1.00
Mol. weight 428.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC9210767
UniProt (similar protein)
P0A6C1
Tanimoto
1.000
Target protein
VK055_4925

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 428.49 Da
LogP (Crippen) 0.83
H-bond donors 3
H-bond acceptors 8
TPSA 137.03 Ų
Rotatable bonds 10
Aromatic rings 3 / 3
Heavy atoms 31
Fraction sp³ C 0.43
Formula C₂₁H₂₈N₆O₄

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 137.0
  • −1 ≤ LogP ≤ 5 0.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 428.5
  • LogP ≤ 5 0.83
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 137.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCn1c(=O)c2[nH]c(-c3ccc(OCC(=O)NCCN)cc3)nc2n(CCC)c1=O
InChI 
InChI=1S/C21H28N6O4/c1-3-11-26-19-17(20(29)27(12-4-2)21(26)30)24-18(25-19)14-5-7-15(8-6-14)31-13-16(28)23-10-9-22/h5-8H,3-4,9-13,22H2,1-2H3,(H,23,28)(H,24,25)
InChIKey 
FIQGIOAELHTLHM-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
XAC
Homolog
P0A6C1

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4925.

PDB 1

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

Ligand PDB entry

ChEMBL 64

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

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)