Ligand profile

6NK

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5jt5 UniProt P28720 Formula C₁₄H₁₉N₅O₂
Mol. weight 289.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6NK
PDB
5jt5
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.34 Da
LogP (Crippen) 0.41
H-bond donors 3
H-bond acceptors 5
TPSA 96.27 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.43
Formula C₁₄H₁₉N₅O₂

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 96.3
  • −1 ≤ LogP ≤ 5 0.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 289.3
  • LogP ≤ 5 0.41
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 96.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1C(=O)N)[nH]c(n2)NCCN3CCOCC3
InChI 
InChI=1S/C14H19N5O2/c15-13(20)10-1-2-11-12(9-10)18-14(17-11)16-3-4-19-5-7-21-8-6-19/h1-2,9H,3-8H2,(H2,15,20)(H2,16,17,18)
InChIKey 
YAZZCCWYYDHQPD-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
PF01702

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_02055.

PDB 60

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

Ligand PDB entry

ChEMBL 5

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)