Ligand profile

ZINC8627115

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q63342 Formula C₂₀H₂₅N₇O₆
Tanimoto 0.64
Mol. weight 459.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8627115
UniProt (similar protein)
Q63342
Tanimoto
0.635
Target protein
KP13_02906

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 459.46 Da
LogP (Crippen) 0.52
H-bond donors 8
H-bond acceptors 10
TPSA 211.82 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.35
Formula C₂₀H₂₅N₇O₆

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 211.8
  • −1 ≤ LogP ≤ 5 0.52
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 459.5
  • LogP ≤ 5 0.52
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 211.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC(=O)O)C(=O)O)cc1)N2
InChI 
InChI=1S/C20H25N7O6/c21-20-26-16-15(18(31)27-20)24-12(9-23-16)7-8-22-11-3-1-10(2-4-11)17(30)25-13(19(32)33)5-6-14(28)29/h1-4,12-13,22,24H,5-9H2,(H,25,30)(H,28,29)(H,32,33)(H4,21,23,26,27,31)/t12-,13+/m0/s1
InChIKey 
SVEJTXIHPDUQLZ-QWHCGFSZSA-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)