Ligand profile

OEE

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 6y6z UniProt G3XD46 Formula C₁₁H₁₉NO₄
Mol. weight 229.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
OEE
PDB
6y6z
UniProt (similar protein)
G3XD46
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 229.28 Da
LogP (Crippen) 1.93
H-bond donors 2
H-bond acceptors 4
TPSA 75.63 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.64
Formula C₁₁H₁₉NO₄

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 75.6
  • −1 ≤ LogP ≤ 5 1.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 229.3
  • LogP ≤ 5 1.93
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 75.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CC(=C)O)(C=O)NC(=O)OC(C)(C)C
InChI 
InChI=1S/C11H19NO4/c1-8(14)6-11(5,7-13)12-9(15)16-10(2,3)4/h7,14H,1,6H2,2-5H3,(H,12,15)/t11-/m0/s1
InChIKey 
DGQSAFHPNXJDHT-NSHDSACASA-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
PF00905

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_1865.

PDB 24

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

Ligand PDB entry

ChEMBL 4

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)