Ligand profile

B59

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 3h2e UniProt Q81VW8 Formula C₉H₈N₄O₄
Mol. weight 236.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B59
PDB
3h2e
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 236.19 Da
LogP (Crippen) -1.87
H-bond donors 1
H-bond acceptors 7
TPSA 106.82 Ų
Rotatable bonds 1
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.22
Formula C₉H₈N₄O₄

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 106.8
  • −1 ≤ LogP ≤ 5 -1.87
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 236.2
  • LogP ≤ 5 -1.87
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 106.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1C2=C(C(=O)N(C1=O)C)N=C(C(=O)N2)C=O
InChI 
InChI=1S/C9H8N4O4/c1-12-6-5(8(16)13(2)9(12)17)10-4(3-14)7(15)11-6/h3H,1-2H3,(H,11,15)
InChIKey 
LVJCGSZYPTZSMO-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)