Ligand profile

CHEMBL3329317

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₀H₂₀N₆O₃
pchembl 7.62 ~24.0 nM
Mol. weight 392.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3329317
UniProt (similar protein)
P0A0K8
pchembl
7.620 (~24.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 392.42 Da
LogP (Crippen) 3.32
H-bond donors 5
H-bond acceptors 6
TPSA 128.27 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 29
Fraction sp³ C 0.10
Formula C₂₀H₂₀N₆O₃

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 128.3
  • −1 ≤ LogP ≤ 5 3.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 392.4
  • LogP ≤ 5 3.32
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 128.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(Nc2ccc(O)cc2)c(C(=O)Nc2cccnc2)cn1
InChI 
InChI=1S/C20H20N6O3/c1-2-22-20(29)26-18-10-17(24-13-5-7-15(27)8-6-13)16(12-23-18)19(28)25-14-4-3-9-21-11-14/h3-12,27H,2H2,1H3,(H,25,28)(H3,22,23,24,26,29)
InChIKey 
IYJZRZIDVYDIHE-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
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)