Ligand profile

2YV

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q8t UniProt P28720 Formula C₁₇H₁₆N₆O
Mol. weight 320.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YV
PDB
4q8t
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 320.36 Da
LogP (Crippen) 2.04
H-bond donors 4
H-bond acceptors 5
TPSA 112.48 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 24
Fraction sp³ C 0.12
Formula C₁₇H₁₆N₆O

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 112.5
  • −1 ≤ LogP ≤ 5 2.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 320.4
  • LogP ≤ 5 2.04
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 112.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CCNc2[nH]c3cc4c(cc3n2)N=C(NC4=O)N
InChI 
InChI=1S/C17H16N6O/c18-16-20-12-9-14-13(8-11(12)15(24)23-16)21-17(22-14)19-7-6-10-4-2-1-3-5-10/h1-5,8-9H,6-7H2,(H2,19,21,22)(H3,18,20,23,24)
InChIKey 
IGMWKNNADHYQOB-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)