Ligand profile

ZINC12296943

Virtual-screening candidate from ZINC.

Bound to: VK055_1021 — bacterial regulatory, gntR family protein

Via homolog UniProt C5CSP2 Formula C₂₆H₃₀N₄O₂
Tanimoto 0.69
Mol. weight 430.55 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12296943
UniProt (similar protein)
C5CSP2
Tanimoto
0.692
Target protein
VK055_1021

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 430.55 Da
LogP (Crippen) 4.23
H-bond donors 4
H-bond acceptors 2
TPSA 89.78 Ų
Rotatable bonds 11
Aromatic rings 4 / 4
Heavy atoms 32
Fraction sp³ C 0.31
Formula C₂₆H₃₀N₄O₂

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 89.8
  • −1 ≤ LogP ≤ 5 4.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 430.6
  • LogP ≤ 5 4.23
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 2
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 89.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(CCCc1c[nH]c2ccccc12)NCCNC(=O)CCCc1c[nH]c2ccccc12
InChI 
InChI=1S/C26H30N4O2/c31-25(13-5-7-19-17-29-23-11-3-1-9-21(19)23)27-15-16-28-26(32)14-6-8-20-18-30-24-12-4-2-10-22(20)24/h1-4,9-12,17-18,29-30H,5-8,13-16H2,(H,27,31)(H,28,32)
InChIKey 
SQVVVWVLSJGFBD-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
3IB
Homolog
C5CSP2

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_1021.

PDB 12

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)