Ligand profile

VRT

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

Bound to: HT085_RS00030 — leucine--tRNA ligase

Via homolog PDB 5onh UniProt P07813 Formula C₁₅H₂₃N₇O₄
Mol. weight 365.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VRT
PDB
5onh
UniProt (similar protein)
P07813
Target protein
HT085_RS00030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 365.39 Da
LogP (Crippen) -1.73
H-bond donors 5
H-bond acceptors 10
TPSA 174.43 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.60
Formula C₁₅H₂₃N₇O₄

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 174.4
  • −1 ≤ LogP ≤ 5 -1.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 365.4
  • LogP ≤ 5 -1.73
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 174.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC(C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)CO)O)N
InChI 
InChI=1S/C15H23N7O4/c1-2-3-7(16)14(25)21-9-11(24)8(4-23)26-15(9)22-6-20-10-12(17)18-5-19-13(10)22/h5-9,11,15,23-24H,2-4,16H2,1H3,(H,21,25)(H2,17,18,19)/t7?,8-,9-,11-,15-/m1/s1
InChIKey 
NWKNSTYARDJRIZ-ZRIALKDISA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF13603

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00030.

PDB 20

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

Ligand PDB entry

ChEMBL 21

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)