Ligand profile

NE8

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5i07 UniProt P28720 Formula C₁₇H₁₅N₅O
Mol. weight 305.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NE8
PDB
5i07
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 305.34 Da
LogP (Crippen) 2.17
H-bond donors 3
H-bond acceptors 4
TPSA 100.45 Ų
Rotatable bonds 3
Aromatic rings 4 / 4
Heavy atoms 23
Fraction sp³ C 0.12
Formula C₁₇H₁₅N₅O

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 100.5
  • −1 ≤ LogP ≤ 5 2.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 305.3
  • LogP ≤ 5 2.17
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 100.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CCc2c3c(cc4c2N=C(NC4=O)N)[nH]cn3
InChI 
InChI=1S/C17H15N5O/c18-17-21-14-11(7-6-10-4-2-1-3-5-10)15-13(19-9-20-15)8-12(14)16(23)22-17/h1-5,8-9H,6-7H2,(H,19,20)(H3,18,21,22,23)
InChIKey 
PBZAIUVFRISTSZ-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)