Ligand profile

TSB

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

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog PDB 1evl UniProt P0A8M3 Formula C₁₄H₂₁N₇O₈S
Mol. weight 447.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TSB
PDB
1evl
UniProt (similar protein)
P0A8M3
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 447.43 Da
LogP (Crippen) -3.89
H-bond donors 6
H-bond acceptors 14
TPSA 238.03 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.57
Formula C₁₄H₂₁N₇O₈S

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 238.0
  • −1 ≤ LogP ≤ 5 -3.89
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 447.4
  • LogP ≤ 5 -3.89
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 238.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]([C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N)O
InChI 
InChI=1S/C14H21N7O8S/c1-5(22)7(15)13(25)20-30(26,27)28-2-6-9(23)10(24)14(29-6)21-4-19-8-11(16)17-3-18-12(8)21/h3-7,9-10,14,22-24H,2,15H2,1H3,(H,20,25)(H2,16,17,18)/t5-,6-,7+,9-,10-,14-/m1/s1
InChIKey 
UPVAPSGKXAAHBG-CKTDUXNWSA-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
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 11

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 50

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

Compound Similarity (Tanimoto)