Ligand profile

PRF

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 1p0e UniProt P28720 Formula C₇H₉N₅O
Mol. weight 179.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PRF
PDB
1p0e
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 179.18 Da
LogP (Crippen) -0.71
H-bond donors 4
H-bond acceptors 4
TPSA 113.58 Ų
Rotatable bonds 1
Aromatic rings 2 / 2
Heavy atoms 13
Fraction sp³ C 0.14
Formula C₇H₉N₅O

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 113.6
  • −1 ≤ LogP ≤ 5 -0.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 179.2
  • LogP ≤ 5 -0.71
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 113.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c2c([nH]1)N=C(NC2=O)N)CN
InChI 
InChI=1S/C7H9N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h2H,1,8H2,(H4,9,10,11,12,13)
InChIKey 
MEYMBLGOKYDGLZ-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)