Ligand profile

4FM

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

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

Via homolog PDB 4yq0 UniProt P43912 Formula C₁₀H₉ClN₄O₂
Mol. weight 252.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4FM
PDB
4yq0
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 252.66 Da
LogP (Crippen) 1.24
H-bond donors 2
H-bond acceptors 5
TPSA 94.04 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.10
Formula C₁₀H₉ClN₄O₂

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 94.0
  • −1 ≤ LogP ≤ 5 1.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 252.7
  • LogP ≤ 5 1.24
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 94.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CNC(=O)c2c(non2)N)Cl
InChI 
InChI=1S/C10H9ClN4O2/c11-7-3-1-6(2-4-7)5-13-10(16)8-9(12)15-17-14-8/h1-4H,5H2,(H2,12,15)(H,13,16)
InChIKey 
WIWIWZDRJHCWJZ-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)