Ligand profile

B56

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 3h26 UniProt Q81VW8 Formula C₈H₉N₅O₃
Mol. weight 223.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B56
PDB
3h26
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 223.19 Da
LogP (Crippen) -1.04
H-bond donors 3
H-bond acceptors 6
TPSA 124.67 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.25
Formula C₈H₉N₅O₃

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 124.7
  • −1 ≤ LogP ≤ 5 -1.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 223.2
  • LogP ≤ 5 -1.04
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 124.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CC(=NC2=C1N=C(NC2=O)N)C(=O)O
InChI 
InChI=1S/C8H9N5O3/c1-13-2-3(7(15)16)10-4-5(13)11-8(9)12-6(4)14/h2H2,1H3,(H,15,16)(H3,9,11,12,14)
InChIKey 
LLLLJZKILITAII-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
PF00809

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_03124.

PDB 46

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

Ligand PDB entry

ChEMBL 26

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)