Ligand profile

H2L

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

Bound to: KP13_04673 — phenylalanyl-tRNA synthetase alpha subunit

Via homolog PDB 7db7 UniProt P9WFU3 Formula C₂₀H₁₉N₅O₃S₂
Mol. weight 441.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
H2L
PDB
7db7
UniProt (similar protein)
P9WFU3
Target protein
KP13_04673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.54 Da
LogP (Crippen) 3.79
H-bond donors 4
H-bond acceptors 5
TPSA 115.98 Ų
Rotatable bonds 7
Aromatic rings 4 / 4
Heavy atoms 30
Fraction sp³ C 0.10
Formula C₂₀H₁₉N₅O₃S₂

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 116.0
  • −1 ≤ LogP ≤ 5 3.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 441.5
  • LogP ≤ 5 3.79
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 116.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c(c[nH]2)CCNS(=O)(=O)c3cccc(c3)NC(=O)Nc4nccs4
InChI 
InChI=1S/C20H19N5O3S2/c26-19(25-20-21-10-11-29-20)24-15-4-3-5-16(12-15)30(27,28)23-9-8-14-13-22-18-7-2-1-6-17(14)18/h1-7,10-13,22-23H,8-9H2,(H2,21,24,25,26)
InChIKey 
NYYVMDXWTXBRNW-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)