Ligand profile

H2R

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

Bound to: KP13_04673 — phenylalanyl-tRNA synthetase alpha subunit

Via homolog PDB 7db8 UniProt P9WFU3 Formula C₂₄H₂₃F₃N₄O₂
Mol. weight 456.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H2R
PDB
7db8
UniProt (similar protein)
P9WFU3
Target protein
KP13_04673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 456.47 Da
LogP (Crippen) 5.77
H-bond donors 1
H-bond acceptors 4
TPSA 67.35 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.29
Formula C₂₄H₂₃F₃N₄O₂

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 67.3
  • −1 ≤ LogP ≤ 5 5.77
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 456.5
  • LogP ≤ 5 5.77
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 67.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)Oc2ccc(cn2)C(F)(F)F)CC3CCN(CC3)C(=O)Nc4cccnc4
InChI 
InChI=1S/C24H23F3N4O2/c25-24(26,27)19-6-7-22(29-15-19)33-21-5-1-3-18(14-21)13-17-8-11-31(12-9-17)23(32)30-20-4-2-10-28-16-20/h1-7,10,14-17H,8-9,11-13H2,(H,30,32)
InChIKey 
NBOJHRYUGLRASX-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)