Ligand profile

D0H

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

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 6f94 UniProt P0AES6 Formula C₂₃H₂₅N₅O₂
Mol. weight 403.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D0H
PDB
6f94
UniProt (similar protein)
P0AES6
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 403.49 Da
LogP (Crippen) 4.84
H-bond donors 4
H-bond acceptors 4
TPSA 95.15 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 30
Fraction sp³ C 0.17
Formula C₂₃H₂₅N₅O₂

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 95.2
  • −1 ≤ LogP ≤ 5 4.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 403.5
  • LogP ≤ 5 4.84
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 95.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1cc(c(cn1)C(=O)Nc2cccc(c2)C)Nc3cccc(c3)C
InChI 
InChI=1S/C23H25N5O2/c1-4-24-23(30)28-21-13-20(26-17-9-5-7-15(2)11-17)19(14-25-21)22(29)27-18-10-6-8-16(3)12-18/h5-14H,4H2,1-3H3,(H,27,29)(H3,24,25,26,28,30)
InChIKey 
XQEFOQFUHGWPSD-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
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 87

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

Ligand PDB entry

ChEMBL 100

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)