Ligand profile

CHEMBL3735341

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog UniProt P0A0K8 Formula C₂₁H₂₁N₉O₂
pchembl 8.00 ~10.0 nM
Mol. weight 431.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL3735341
UniProt (similar protein)
P0A0K8
pchembl
8.000 (~10.0 nM)
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 431.46 Da
LogP (Crippen) 2.03
H-bond donors 3
H-bond acceptors 8
TPSA 131.65 Ų
Rotatable bonds 6
Aromatic rings 4 / 5
Heavy atoms 32
Fraction sp³ C 0.24
Formula C₂₁H₂₁N₉O₂

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 131.7
  • −1 ≤ LogP ≤ 5 2.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 431.5
  • LogP ≤ 5 2.03
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 131.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cn(-c2ncccn2)c2cc(-n3cnc(C(=O)NC4CC4)c3)cnc12
InChI 
InChI=1S/C21H21N9O2/c1-2-22-21(32)28-15-11-30(20-23-6-3-7-24-20)17-8-14(9-25-18(15)17)29-10-16(26-12-29)19(31)27-13-4-5-13/h3,6-13H,2,4-5H2,1H3,(H,27,31)(H2,22,28,32)
InChIKey 
YKRKUHQNUKKNJV-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)