Ligand profile

JA5

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

Bound to: KP13_02423 — tRNA (guanine-N(1)-)-methyltransferase

Via homolog PDB 6qox UniProt B1MDI3 Formula C₉H₉NO₃S
Mol. weight 211.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JA5
PDB
6qox
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 211.24 Da
LogP (Crippen) 1.51
H-bond donors 2
H-bond acceptors 4
TPSA 62.32 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.22
Formula C₉H₉NO₃S

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 62.3
  • −1 ≤ LogP ≤ 5 1.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 211.2
  • LogP ≤ 5 1.51
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 62.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)c1cc2cc(sc2[nH]1)CO
InChI 
InChI=1S/C9H9NO3S/c1-13-9(12)7-3-5-2-6(4-11)14-8(5)10-7/h2-3,10-11H,4H2,1H3
InChIKey 
FJDCCIDVLHNLOW-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
PF01746

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_02423.

PDB 88

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

Ligand PDB entry

ChEMBL 38

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)