Ligand profile

BDI

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 2z1w UniProt P28720 Formula C₉H₁₂N₄O₂
Mol. weight 208.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BDI
PDB
2z1w
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 208.22 Da
LogP (Crippen) 0.28
H-bond donors 3
H-bond acceptors 3
TPSA 94.40 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.44
Formula C₉H₁₂N₄O₂

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 94.4
  • −1 ≤ LogP ≤ 5 0.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 208.2
  • LogP ≤ 5 0.28
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 94.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCc1[nH]c2c(n1)C(=O)NNC2=O
InChI 
InChI=1S/C9H12N4O2/c1-2-3-4-5-10-6-7(11-5)9(15)13-12-8(6)14/h2-4H2,1H3,(H,10,11)(H,12,14)(H,13,15)
InChIKey 
DQHJYYALMHIEAH-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)