Ligand profile

ZINC13377742

Virtual-screening candidate from ZINC.

Bound to: VK055_3902 — translation initiation factor IF-2

Via homolog UniProt P46199 Formula C₁₂H₃₀N₄

Tanimoto 0.86

Mol. weight 230.40 Da

Permeability High

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: ZINC13377742
UniProt (similar protein): P46199
Tanimoto: 0.857
Target protein: VK055_3902

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 230.40 Da

LogP (Crippen) 0.42

H-bond donors 4

H-bond acceptors 4

TPSA 76.10 Å²

Rotatable bonds 13

Aromatic rings 0 / 0

Heavy atoms 16

Fraction sp³ C 1.00

Formula C₁₂H₃₀N₄

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 76.1
−1 ≤ LogP ≤ 5 0.42

Lipinski's Rule of Five Pass 0 violations

MW ≤ 500 Da 230.4
LogP ≤ 5 0.42
H-bond donors ≤ 5 4
H-bond acceptors ≤ 10 4

Veber's rules Fail

Rotatable bonds ≤ 10 13
TPSA ≤ 140 Å² 76.1

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

NCCCCNCCCCNCCCCN

InChI

InChI=1S/C12H30N4/c13-7-1-3-9-15-11-5-6-12-16-10-4-2-8-14/h15-16H,1-14H2

InChIKey

RPSHOHKFHRFBAZ-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: SPM
Homolog: P46199

External resources

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

ZINC ZINC15 ZINC13377742 →
ZINC ZINC20 ZINC13377742 →
UniProt UniProt P46199 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “ZINC13377742”) →

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3902.

PDB 11

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)