Ligand profile

BDE

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

Bound to: KP13_01799 — (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase

Via homolog PDB 2glp UniProt O25928 Formula C₁₃H₉Br₂N₃O₃
Mol. weight 415.04 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
BDE
PDB
2glp
UniProt (similar protein)
O25928
Target protein
KP13_01799

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.04 Da
LogP (Crippen) 2.78
H-bond donors 3
H-bond acceptors 5
TPSA 94.81 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 21
Fraction sp³ C 0.00
Formula C₁₃H₉Br₂N₃O₃

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 94.8
  • −1 ≤ LogP ≤ 5 2.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 415.0
  • LogP ≤ 5 2.78
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 94.8
PAINS Alert

Matches PAINS filter: hzone_phenol_A(479). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cnc1)C(=O)N/N=C/c2cc(c(c(c2O)Br)O)Br
InChI 
InChI=1S/C13H9Br2N3O3/c14-9-4-8(11(19)10(15)12(9)20)6-17-18-13(21)7-2-1-3-16-5-7/h1-6,19-20H,(H,18,21)/b17-6+
InChIKey 
PYVJEAZDEZTGIS-UBKPWBPPSA-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
PF07977

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_01799.

PDB 20

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

Ligand PDB entry

ChEMBL 5

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)