Ligand profile

2NM

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

Bound to: KP13_04673 — phenylalanyl-tRNA synthetase alpha subunit

Via homolog PDB 4p75 UniProt Q9I0A3 Formula C₁₁H₉F₃N₂O
Mol. weight 242.20 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2NM
PDB
4p75
UniProt (similar protein)
Q9I0A3
Target protein
KP13_04673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 242.20 Da
LogP (Crippen) 3.10
H-bond donors 1
H-bond acceptors 2
TPSA 37.91 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.18
Formula C₁₁H₉F₃N₂O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 37.9
  • −1 ≤ LogP ≤ 5 3.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 242.2
  • LogP ≤ 5 3.10
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 37.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cccc(c1)c2cc([nH]n2)C(F)(F)F
InChI 
InChI=1S/C11H9F3N2O/c1-17-8-4-2-3-7(5-8)9-6-10(16-15-9)11(12,13)14/h2-6H,1H3,(H,15,16)
InChIKey 
ZYXHXNGIOSVJRA-UHFFFAOYSA-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
PF01409

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_04673.

PDB 7

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

Ligand PDB entry

ChEMBL 1

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)