Ligand profile

E89

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5i06 UniProt P28720 Formula C₁₈H₁₇N₅O₂
Mol. weight 335.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E89
PDB
5i06
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.37 Da
LogP (Crippen) 2.18
H-bond donors 3
H-bond acceptors 5
TPSA 109.68 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 25
Fraction sp³ C 0.17
Formula C₁₈H₁₇N₅O₂

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 109.7
  • −1 ≤ LogP ≤ 5 2.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.4
  • LogP ≤ 5 2.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 109.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)CCc2c3c(cc4c2N=C(NC4=O)N)[nH]cn3
InChI 
InChI=1S/C18H17N5O2/c1-25-11-5-2-10(3-6-11)4-7-12-15-13(17(24)23-18(19)22-15)8-14-16(12)21-9-20-14/h2-3,5-6,8-9H,4,7H2,1H3,(H,20,21)(H3,19,22,23,24)
InChIKey 
UKRVQKUVWNDGMN-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)