Ligand profile

VB3

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

Bound to: KP13_04673 — phenylalanyl-tRNA synthetase alpha subunit

Via homolog PDB 6oz5 UniProt P08312 Formula C₁₆H₂₅NO
Mol. weight 247.38 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
VB3
PDB
6oz5
UniProt (similar protein)
P08312
Target protein
KP13_04673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 247.38 Da
LogP (Crippen) 3.84
H-bond donors 2
H-bond acceptors 2
TPSA 32.26 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.62
Formula C₁₆H₂₅NO

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 32.3
  • −1 ≤ LogP ≤ 5 3.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 247.4
  • LogP ≤ 5 3.84
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 32.3
PAINS Alert

Matches PAINS filter: mannich_A(296). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](CC1CCCCC1)NCc2ccccc2O
InChI 
InChI=1S/C16H25NO/c1-13(11-14-7-3-2-4-8-14)17-12-15-9-5-6-10-16(15)18/h5-6,9-10,13-14,17-18H,2-4,7-8,11-12H2,1H3/t13-/m0/s1
InChIKey 
IRWBEPDMVHOCPD-ZDUSSCGKSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01409

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_04673.

PDB 7

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

Ligand PDB entry

ChEMBL 1

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)