Ligand profile

HPA

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

Bound to: KP13_00003 — Ribose operon repressor

Via homolog PDB 1bdh UniProt P0ACP7 Formula C₅H₄N₄O
Mol. weight 136.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HPA
PDB
1bdh
UniProt (similar protein)
P0ACP7
Target protein
KP13_00003

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 136.11 Da
LogP (Crippen) -0.35
H-bond donors 2
H-bond acceptors 3
TPSA 74.43 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 10
Fraction sp³ C 0.00
Formula C₅H₄N₄O

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 74.4
  • −1 ≤ LogP ≤ 5 -0.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 136.1
  • LogP ≤ 5 -0.35
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 74.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)N=CNC2=O
InChI 
InChI=1S/C5H4N4O/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H2,6,7,8,9,10)
InChIKey 
FDGQSTZJBFJUBT-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
PF13377

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_00003.

PDB 5

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

Ligand PDB entry

ZINC 37

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

Compound Similarity (Tanimoto)