Ligand profile

XYD

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

Bound to: KP13_02342 — Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Via homolog PDB 1l4l UniProt Q05603 Formula C₈H₁₁N
Mol. weight 121.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XYD
PDB
1l4l
UniProt (similar protein)
Q05603
Target protein
KP13_02342

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 121.18 Da
LogP (Crippen) 1.89
H-bond donors 1
H-bond acceptors 1
TPSA 26.02 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.25
Formula C₈H₁₁N

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 26.0
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 121.2
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 26.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(c(c1)N)C
InChI 
InChI=1S/C8H11N/c1-6-3-4-7(2)8(9)5-6/h3-5H,9H2,1-2H3
InChIKey 
VOWZNBNDMFLQGM-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
PF02277

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_02342.

PDB 25

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)