Ligand profile

B58

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 3h2c UniProt Q81VW8 Formula C₅H₆N₆
Mol. weight 150.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B58
PDB
3h2c
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 150.14 Da
LogP (Crippen) -0.48
H-bond donors 3
H-bond acceptors 5
TPSA 106.50 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 11
Fraction sp³ C 0.00
Formula C₅H₆N₆

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 106.5
  • −1 ≤ LogP ≤ 5 -0.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 150.1
  • LogP ≤ 5 -0.48
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 106.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)c(nnc2N)N
InChI 
InChI=1S/C5H6N6/c6-4-2-3(9-1-8-2)5(7)11-10-4/h1H,(H2,6,10)(H2,7,11)(H,8,9)
InChIKey 
UMLCZSAOYUCVKU-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)