Ligand profile

2J1

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

Bound to: HT085_RS00010 — DNA polymerase III subunit beta

Via homolog PDB 4n99 UniProt P0A988 Formula C₁₃H₁₂ClNO₂
Mol. weight 249.70 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
2J1
PDB
4n99
UniProt (similar protein)
P0A988
Target protein
HT085_RS00010

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 249.70 Da
LogP (Crippen) 3.40
H-bond donors 2
H-bond acceptors 1
TPSA 53.09 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 17
Fraction sp³ C 0.31
Formula C₁₃H₁₂ClNO₂

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 53.1
  • −1 ≤ LogP ≤ 5 3.40
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 249.7
  • LogP ≤ 5 3.40
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 53.1
PAINS Alert

Matches PAINS filter: indol_3yl_alk(461). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(cc(c1Cl)C(=O)O)[nH]c3c2CCCC3
InChI 
InChI=1S/C13H12ClNO2/c14-10-5-8-7-3-1-2-4-11(7)15-12(8)6-9(10)13(16)17/h5-6,15H,1-4H2,(H,16,17)
InChIKey 
QPXAEUZWZDSOOF-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
PF02767' 'PF02768

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00010.

PDB 18

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)