Ligand profile

KRM

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

Bound to: KP13_00293 — 2-dehydro-3-deoxygluconokinase

Via homolog PDB 2xtb UniProt Q584S0 Formula C₁₉H₁₉N₃O₂
Mol. weight 321.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
KRM
PDB
2xtb
UniProt (similar protein)
Q584S0
Target protein
KP13_00293

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 321.38 Da
LogP (Crippen) 3.71
H-bond donors 1
H-bond acceptors 4
TPSA 50.38 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 24
Fraction sp³ C 0.21
Formula C₁₉H₁₉N₃O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 50.4
  • −1 ≤ LogP ≤ 5 3.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 321.4
  • LogP ≤ 5 3.71
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 50.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)Oc2ccc(cc2)c3cc(n[nH]3)N4CCOCC4
InChI 
InChI=1S/C19H19N3O2/c1-2-4-16(5-3-1)24-17-8-6-15(7-9-17)18-14-19(21-20-18)22-10-12-23-13-11-22/h1-9,14H,10-13H2,(H,20,21)
InChIKey 
WQWBZRVAFAMASC-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
PDB
Binding sites
PF00294

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_00293.

PDB 6

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)