Ligand profile

ZINC169753878

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q02RL6 Formula C₂₄H₂₅N₅O₂
Tanimoto 0.81
Mol. weight 415.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC169753878
UniProt (similar protein)
Q02RL6
Tanimoto
0.812
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.50 Da
LogP (Crippen) 3.97
H-bond donors 3
H-bond acceptors 4
TPSA 86.04 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 31
Fraction sp³ C 0.25
Formula C₂₄H₂₅N₅O₂

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 86.0
  • −1 ≤ LogP ≤ 5 3.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 415.5
  • LogP ≤ 5 3.97
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 86.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(-c2cc(N3CCC[C@H](NC(=O)c4cc5ccccc5[nH]4)C3)[nH]n2)cc1
InChI 
InChI=1S/C24H25N5O2/c1-31-19-10-8-16(9-11-19)21-14-23(28-27-21)29-12-4-6-18(15-29)25-24(30)22-13-17-5-2-3-7-20(17)26-22/h2-3,5,7-11,13-14,18,26H,4,6,12,15H2,1H3,(H,25,30)(H,27,28)/t18-/m0/s1
InChIKey 
SXLBIYVYVSPHRV-SFHVURJKSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
9WO
Homolog
Q02RL6

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 89

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)