Ligand profile

B63

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

Bound to: KP13_03124 — Dihydropteroate synthase type-1

Via homolog PDB 3h2o UniProt Q81VW8 Formula C₁₅H₁₆N₆O₃
Mol. weight 328.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B63
PDB
3h2o
UniProt (similar protein)
Q81VW8
Target protein
KP13_03124

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 328.33 Da
LogP (Crippen) 1.05
H-bond donors 5
H-bond acceptors 7
TPSA 145.49 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.20
Formula C₁₅H₁₆N₆O₃

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 145.5
  • −1 ≤ LogP ≤ 5 1.05
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 328.3
  • LogP ≤ 5 1.05
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 145.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)O)NCCC2=NC3=C(NC2)N=C(NC3=O)N
InChI 
InChI=1S/C15H16N6O3/c16-15-20-12-11(13(22)21-15)19-10(7-18-12)5-6-17-9-3-1-8(2-4-9)14(23)24/h1-4,17H,5-7H2,(H,23,24)(H4,16,18,20,21,22)
InChIKey 
KCMJLKPNBXLNNJ-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)