Ligand profile

B2M

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

Bound to: KP13_03634 — Maltose O-acetyltransferase

Via homolog PDB 3dho UniProt P50870 Formula C₁₈H₁₂BrCl₂N₃O₂
Mol. weight 453.12 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
B2M
PDB
3dho
UniProt (similar protein)
P50870
Target protein
KP13_03634

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 453.12 Da
LogP (Crippen) 5.08
H-bond donors 2
H-bond acceptors 4
TPSA 74.58 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.06
Formula C₁₈H₁₂BrCl₂N₃O₂

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 74.6
  • −1 ≤ LogP ≤ 5 5.08
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 453.1
  • LogP ≤ 5 5.08
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.6
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 
Cc1cc(c2cc(ccc2n1)Br)C(=O)N/N=C\c3cc(cc(c3O)Cl)Cl
InChI 
InChI=1S/C18H12BrCl2N3O2/c1-9-4-14(13-6-11(19)2-3-16(13)23-9)18(26)24-22-8-10-5-12(20)7-15(21)17(10)25/h2-8,25H,1H3,(H,24,26)/b22-8-
InChIKey 
JOLMQMRBSITJES-UYOCIXKTSA-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
PF00132

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_03634.

PDB 5

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

Ligand PDB entry

ZINC 27

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)