Binder profile

CBD

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

Bound to: PA1962 — FMN-dependent NADH-azoreductase

Via homolog PDB 3w78 UniProt C0STY1 C29H20ClN7O11S3
Mol. weight 774.17 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CBD
PDB
3w78
UniProt (similar protein)
C0STY1
Target protein
PA1962

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 774.17 Da
LogP (Crippen) 3.85
H-bond donors 7
H-bond acceptors 15
TPSA 298.03 Ų
Rotatable bonds 9
Aromatic rings 5 / 6
Heavy atoms 51
Fraction sp³ C 0.00
Formula C29H20ClN7O11S3

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 Fail 3 violations
  • MW ≤ 500 Da 774.2
  • LogP ≤ 5 3.85
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 298.0
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)C(=O)c3c(cc(c(c3C2=O)N)S(=O)(=O)O)Nc4ccc(c(c4)S(=O)(=O)O)Nc5nc(nc(n5)Cl)Nc6ccccc6S(=O)(=O)O
InChI 
InChI=1S/C29H20ClN7O11S3/c30-27-35-28(33-16-7-3-4-8-19(16)49(40,41)42)37-29(36-27)34-17-10-9-13(11-20(17)50(43,44)45)32-18-12-21(51(46,47)48)24(31)23-22(18)25(38)14-5-1-2-6-15(14)26(23)39/h1-12,32H,31H2,(H,40,41,42)(H,43,44,45)(H,46,47,48)(H2,33,34,35,36,37)
InChIKey 
YKCWQPZFAFZLBI-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02525

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA1962.

PDB 8

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)