Binder profile

3II

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

Bound to: PA2250 — branched-chain alpha-keto acid dehydrogenase complex dihydrolipoyl dehydrogenase

Via homolog PDB 3ii4 UniProt P9WHH9 C32H34Cl2N4O5
Mol. weight 625.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3II
PDB
3ii4
UniProt (similar protein)
P9WHH9
Target protein
PA2250

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 625.55 Da
LogP (Crippen) 4.65
H-bond donors 1
H-bond acceptors 6
TPSA 91.42 Ų
Rotatable bonds 9
Aromatic rings 3 / 5
Heavy atoms 43
Fraction sp³ C 0.34
Formula C32H34Cl2N4O5

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.

Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 625.6
  • LogP ≤ 5 4.65
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 91.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccccc4)CC(=O)NCCc5ccc(cc5Cl)Cl
InChI 
InChI=1S/C32H34Cl2N4O5/c1-42-25-10-11-26(28(19-25)43-2)30(40)36-16-13-32(14-17-36)31(41)37(21-38(32)24-6-4-3-5-7-24)20-29(39)35-15-12-22-8-9-23(33)18-27(22)34/h3-11,18-19H,12-17,20-21H2,1-2H3,(H,35,39)
InChIKey 
TWOVSEVREOPZGM-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2 search.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00070' 'PF02852' 'PF12831

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2250.

PDB 4

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)