Ligand profile

EFY

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

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

Via homolog PDB 4yq2 UniProt P43912 Formula C₂₅H₂₉N₃O₃
Mol. weight 419.53 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EFY
PDB
4yq2
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 419.53 Da
LogP (Crippen) 4.60
H-bond donors 2
H-bond acceptors 4
TPSA 84.23 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 31
Fraction sp³ C 0.40
Formula C₂₅H₂₉N₃O₃

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 84.2
  • −1 ≤ LogP ≤ 5 4.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 419.5
  • LogP ≤ 5 4.60
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 84.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)c1cccc(c1)C(=O)NCC2(CCCC2)NC(=O)c3cccc4c3con4
InChI 
InChI=1S/C25H29N3O3/c1-24(2,3)18-9-6-8-17(14-18)22(29)26-16-25(12-4-5-13-25)27-23(30)19-10-7-11-21-20(19)15-31-28-21/h6-11,14-15H,4-5,12-13,16H2,1-3H3,(H,26,29)(H,27,30)
InChIKey 
ZVPHHRCZSPAOCC-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)