Ligand profile

G9Z

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

Bound to: VK055_3568 — dppA

Via homolog PDB 6hlx UniProt O50260 Formula C₁₁H₁₇NO₈
Mol. weight 291.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G9Z
PDB
6hlx
UniProt (similar protein)
O50260
Target protein
VK055_3568

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 291.26 Da
LogP (Crippen) -3.73
H-bond donors 6
H-bond acceptors 7
TPSA 158.76 Ų
Rotatable bonds 7
Aromatic rings 0 / 1
Heavy atoms 20
Fraction sp³ C 0.64
Formula C₁₁H₁₇NO₈

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 158.8
  • −1 ≤ LogP ≤ 5 -3.73
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 291.3
  • LogP ≤ 5 -3.73
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CC(=O)N([C@@H]1C(=O)O)C[C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O
InChI 
InChI=1S/C11H17NO8/c13-4-7(15)10(18)9(17)6(14)3-12-5(11(19)20)1-2-8(12)16/h1-2,5-7,9-10,13-15,17-18H,3-4H2,(H,19,20)/t5-,6+,7+,9+,10+/m0/s1
InChIKey 
WYIHPABVKQQJFB-SZWOQXJISA-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
PF00496

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3568.

PDB 17

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)