Ligand profile

9YN

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

Bound to: HT085_RS00030 — leucine--tRNA ligase

Via homolog PDB 5on3 UniProt P07813 Formula C₁₆H₂₅N₇O₄
Mol. weight 379.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9YN
PDB
5on3
UniProt (similar protein)
P07813
Target protein
HT085_RS00030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 379.42 Da
LogP (Crippen) -1.48
H-bond donors 5
H-bond acceptors 10
TPSA 174.43 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.62
Formula C₁₆H₂₅N₇O₄

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 -1.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 379.4
  • LogP ≤ 5 -1.48
  • 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 
CC(C)C[C@@H](C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)CO)O)N
InChI 
InChI=1S/C16H25N7O4/c1-7(2)3-8(17)15(26)22-10-12(25)9(4-24)27-16(10)23-6-21-11-13(18)19-5-20-14(11)23/h5-10,12,16,24-25H,3-4,17H2,1-2H3,(H,22,26)(H2,18,19,20)/t8-,9+,10+,12+,16+/m0/s1
InChIKey 
NMAIYRCXMINABF-GBPQWNHNSA-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)