Ligand profile

ZINC8655682

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q63342 Formula C₂₁H₂₅N₇O₇
Tanimoto 0.63
Mol. weight 487.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8655682
UniProt (similar protein)
Q63342
Tanimoto
0.628
Target protein
KP13_02906

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 487.47 Da
LogP (Crippen) -0.34
H-bond donors 7
H-bond acceptors 9
TPSA 219.84 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 35
Fraction sp³ C 0.33
Formula C₂₁H₂₅N₇O₇

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 219.8
  • −1 ≤ LogP ≤ 5 -0.34
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 487.5
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 219.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc1)CN2
InChI 
InChI=1S/C21H25N7O7/c22-21-26-17-16(19(33)27-21)28(10-29)13(9-24-17)7-8-23-12-3-1-11(2-4-12)18(32)25-14(20(34)35)5-6-15(30)31/h1-4,10,13-14,23H,5-9H2,(H,25,32)(H,30,31)(H,34,35)(H4,22,24,26,27,33)/t13-,14-/m0/s1
InChIKey 
GOPPVQOEWUBPLM-KBPBESRZSA-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)