Ligand profile

ODZ

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 6y6u UniProt G3XD46 Formula C₁₄H₁₇NO₄
Mol. weight 263.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ODZ
PDB
6y6u
UniProt (similar protein)
G3XD46
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 263.29 Da
LogP (Crippen) 1.47
H-bond donors 3
H-bond acceptors 4
TPSA 86.63 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 19
Fraction sp³ C 0.29
Formula C₁₄H₁₇NO₄

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 86.6
  • −1 ≤ LogP ≤ 5 1.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 263.3
  • LogP ≤ 5 1.47
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 86.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CC(=C)O)(C=O)NC(=O)Cc1ccc(cc1)O
InChI 
InChI=1S/C14H17NO4/c1-10(17)8-14(2,9-16)15-13(19)7-11-3-5-12(18)6-4-11/h3-6,9,17-18H,1,7-8H2,2H3,(H,15,19)/t14-/m0/s1
InChIKey 
RSUSHGHDXWZFTH-AWEZNQCLSA-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)