Ligand profile

4GM

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

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

Via homolog PDB 4yqb UniProt P43912 Formula C₁₃H₁₃N₃O₂
Mol. weight 243.27 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
4GM
PDB
4yqb
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 243.27 Da
LogP (Crippen) 1.50
H-bond donors 3
H-bond acceptors 4
TPSA 88.24 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 18
Fraction sp³ C 0.08
Formula C₁₃H₁₃N₃O₂

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 88.2
  • −1 ≤ LogP ≤ 5 1.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 243.3
  • LogP ≤ 5 1.50
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 88.2
PAINS Alert

Matches PAINS filter: mannich_A(296). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)CNc2ccc(cn2)C(=O)N)O
InChI 
InChI=1S/C13H13N3O2/c14-13(18)10-5-6-12(16-8-10)15-7-9-3-1-2-4-11(9)17/h1-6,8,17H,7H2,(H2,14,18)(H,15,16)
InChIKey 
NNNVBOGULIXEBW-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)