Ligand profile

ZINC4654270

Virtual-screening candidate from ZINC.

Bound to: KP13_02906 — L-2-hydroxyglutarate oxidase LhgO

Via homolog UniProt Q63342 Formula C₂₀H₂₁N₇O₇
Tanimoto 0.59
Mol. weight 471.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4654270
UniProt (similar protein)
Q63342
Tanimoto
0.592
Target protein
KP13_02906

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 471.43 Da
LogP (Crippen) -0.36
H-bond donors 6
H-bond acceptors 8
TPSA 211.05 Ų
Rotatable bonds 7
Aromatic rings 2 / 4
Heavy atoms 34
Fraction sp³ C 0.30
Formula C₂₀H₂₁N₇O₇

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 211.0
  • −1 ≤ LogP ≤ 5 -0.36
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 471.4
  • LogP ≤ 5 -0.36
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 211.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc3)C[C@H]1CN2
InChI 
InChI=1S/C20H21N7O7/c21-19-24-15-14(17(31)25-19)27-11(7-22-15)8-26(20(27)34)10-3-1-9(2-4-10)16(30)23-12(18(32)33)5-6-13(28)29/h1-4,11-12H,5-8H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/t11-,12+/m1/s1
InChIKey 
JSNFRYBHBVDHSG-NEPJUHHUSA-N

Provenance

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

Method
LigQ nearest_k
Query
THG
Homolog
Q63342

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_02906.

PDB 2

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)