Ligand profile

CHEMBL3736056

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₁H₂₁N₇O₂
pchembl 7.89 ~12.9 nM
Mol. weight 403.45 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3736056
UniProt (similar protein)
P0A0K8
pchembl
7.890 (~12.9 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.45 Da
LogP (Crippen) 2.63
H-bond donors 2
H-bond acceptors 7
TPSA 106.73 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 30
Fraction sp³ C 0.19
Formula C₂₁H₂₁N₇O₂

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 106.7
  • −1 ≤ LogP ≤ 5 2.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 403.4
  • LogP ≤ 5 2.63
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 106.7
PAINS Alert

Matches PAINS filter: dyes5A(27). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cn(-c2ncc(C)cn2)c2cc(-c3ccn(C)c(=O)c3)cnc12
InChI 
InChI=1S/C21H21N7O2/c1-4-22-21(30)26-16-12-28(20-24-9-13(2)10-25-20)17-7-15(11-23-19(16)17)14-5-6-27(3)18(29)8-14/h5-12H,4H2,1-3H3,(H2,22,26,30)
InChIKey 
VVTCBHKDMOUUNZ-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)