Ligand profile

WBU

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

Bound to: KP13_00801 — Uracil-DNA glycosylase

Via homolog PDB 4ws6 UniProt P9WFQ9 Formula C₄H₅N₃O₂
Mol. weight 127.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WBU
PDB
4ws6
UniProt (similar protein)
P9WFQ9
Target protein
KP13_00801

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 127.10 Da
LogP (Crippen) -1.35
H-bond donors 3
H-bond acceptors 3
TPSA 91.74 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.00
Formula C₄H₅N₃O₂

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 91.7
  • −1 ≤ LogP ≤ 5 -1.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 127.1
  • LogP ≤ 5 -1.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 91.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(C(=O)NC(=O)N1)N
InChI 
InChI=1S/C4H5N3O2/c5-2-1-6-4(9)7-3(2)8/h1H,5H2,(H2,6,7,8,9)
InChIKey 
BISHACNKZIBDFM-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
PF03167

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_00801.

PDB 15

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

Ligand PDB entry

ChEMBL 1

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)