Ligand profile

CBN

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0AES6 Formula C₃₅H₃₇ClN₂O₁₁
pchembl 8.92 ~1.2 nM
Mol. weight 697.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CBN
UniProt (similar protein)
P0AES6
pchembl
8.920 (~1.2 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 697.14 Da
LogP (Crippen) 5.37
H-bond donors 5
H-bond acceptors 11
TPSA 189.78 Ų
Rotatable bonds 9
Aromatic rings 4 / 5
Heavy atoms 49
Fraction sp³ C 0.34
Formula C₃₅H₃₇ClN₂O₁₁

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 189.8
  • −1 ≤ LogP ≤ 5 5.37
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 697.1
  • LogP ≤ 5 5.37
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 189.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc([nH]1)C(=O)O[C@H]2[C@H]([C@@H](OC([C@@H]2OC)(C)C)Oc3ccc4c(c3Cl)OC(=O)C(=C4O)NC(=O)c5ccc(c(c5)CC=C(C)C)O)O
InChI 
InChI=1S/C35H37ClN2O11/c1-16(2)7-9-18-15-19(10-13-22(18)39)31(42)38-25-26(40)20-11-14-23(24(36)28(20)47-33(25)44)46-34-27(41)29(30(45-6)35(4,5)49-34)48-32(43)21-12-8-17(3)37-21/h7-8,10-15,27,29-30,34,37,39-41H,9H2,1-6H3,(H,38,42)/t27-,29+,30-,34-/m1/s1
InChIKey 
FJAQNRBDVKIIKK-LFLQOBSNSA-N

Provenance

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

Method
LigQ sequence
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF02518

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_00051.

PDB 88

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

Ligand PDB entry

ChEMBL 99

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)