Ligand profile

ZINC2012436

Virtual-screening candidate from ZINC.

Bound to: VK055_4925 — apurinic endonuclease family protein

Via homolog UniProt P0A6C1 Formula C₂₁H₃₁N₅O₃
Tanimoto 1.00
Mol. weight 401.51 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2012436
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 401.51 Da
LogP (Crippen) 1.03
H-bond donors 1
H-bond acceptors 8
TPSA 71.74 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.52
Formula C₂₁H₃₁N₅O₃

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 71.7
  • −1 ≤ LogP ≤ 5 1.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.5
  • LogP ≤ 5 1.03
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 71.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccccc1N1CCN(CCCNc2c(C)c(=O)n(C)c(=O)n2C)CC1
InChI 
InChI=1S/C21H31N5O3/c1-16-19(23(2)21(28)24(3)20(16)27)22-10-7-11-25-12-14-26(15-13-25)17-8-5-6-9-18(17)29-4/h5-6,8-9,22H,7,10-15H2,1-4H3
InChIKey 
HIHZDNKKIUQQSC-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
CHEMBL420060
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)