Ligand profile

CHEMBL3754066

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog UniProt P26639 Formula C₂₈H₄₄N₂O₅
Mol. weight 488.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3754066
UniProt (similar protein)
P26639
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.67 Da
LogP (Crippen) 4.04
H-bond donors 3
H-bond acceptors 6
TPSA 133.64 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 35
Fraction sp³ C 0.75
Formula C₂₈H₄₄N₂O₅

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 133.6
  • −1 ≤ LogP ≤ 5 4.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 488.7
  • LogP ≤ 5 4.04
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 133.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C[C@H](C)C[C@H](C)[C@@H](O)CC(=O)O[C@H]([C@@H]2CCC[C@H]2C(N)=O)C/C=C/C=C(/C#N)[C@H](O)[C@@H](C)C1
InChI 
InChI=1S/C28H44N2O5/c1-17-12-18(2)14-20(4)27(33)21(16-29)8-5-6-11-25(22-9-7-10-23(22)28(30)34)35-26(32)15-24(31)19(3)13-17/h5-6,8,17-20,22-25,27,31,33H,7,9-15H2,1-4H3,(H2,30,34)/b6-5+,21-8-/t17-,18+,19-,20-,22+,23+,24-,25-,27+/m0/s1
InChIKey 
IOHLCKBCGGSSCP-UGKRXNSESA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Curation
pdb_similarity_tanimoto
Binding sites
PF00587

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 27

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)