Ligand profile

ZINC253665472

Virtual-screening candidate from ZINC.

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog UniProt P0A8M3 Formula C₂₈H₄₃NO₆
Tanimoto 1.00
Mol. weight 489.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC253665472
UniProt (similar protein)
P0A8M3
Tanimoto
1.000
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 489.65 Da
LogP (Crippen) 4.64
H-bond donors 3
H-bond acceptors 6
TPSA 127.85 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 35
Fraction sp³ C 0.75
Formula C₂₈H₄₃NO₆

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 127.9
  • −1 ≤ LogP ≤ 5 4.64
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 489.7
  • LogP ≤ 5 4.64
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 127.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C[C@H](C)[C@@H](O)CC(=O)O[C@H]([C@@H]2CCC[C@H]2C(=O)O)CC=CC=C(C#N)[C@H](O)[C@@H](C)C[C@H](C)C1
InChI 
InChI=1S/C28H43NO6/c1-17-12-18(2)14-20(4)27(32)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(33)34)35-26(31)15-24(30)19(3)13-17/h5-6,8,17-20,22-25,27,30,32H,7,9-15H2,1-4H3,(H,33,34)/t17-,18+,19-,20-,22+,23+,24-,25-,27+/m0/s1
InChIKey 
OJCKRNPLOZHAOU-HBJZAWFCSA-N

Provenance

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

Method
LigQ sequence
Query
2CR
Homolog
P0A8M3

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_0276.

PDB 12

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

Ligand PDB entry

ChEMBL 28

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)