Ligand profile

B60

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

Bound to: KP13_03130 — Dihydropteroate synthase type-1

Via homolog PDB 3h2f UniProt Q81VW8 Formula C₇H₉N₅O
Mol. weight 179.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B60
PDB
3h2f
UniProt (similar protein)
Q81VW8
Target protein
KP13_03130

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 179.18 Da
LogP (Crippen) -0.50
H-bond donors 2
H-bond acceptors 5
TPSA 87.37 Ų
Rotatable bonds 0
Aromatic rings 1 / 2
Heavy atoms 13
Fraction sp³ C 0.29
Formula C₇H₉N₅O

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 87.4
  • −1 ≤ LogP ≤ 5 -0.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 179.2
  • LogP ≤ 5 -0.50
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 87.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CC=NC2=C1N=C(NC2=O)N
InChI 
InChI=1S/C7H9N5O/c1-12-3-2-9-4-5(12)10-7(8)11-6(4)13/h2H,3H2,1H3,(H3,8,10,11,13)
InChIKey 
NJYUAWHEKRBMQB-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_03130.

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)