Ligand profile

ZINC4556304

Virtual-screening candidate from ZINC.

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog UniProt Q51504 Formula C₁₅H₁₇N₃O₆
Tanimoto 0.61
Mol. weight 335.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4556304
UniProt (similar protein)
Q51504
Tanimoto
0.609
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.32 Da
LogP (Crippen) -0.08
H-bond donors 3
H-bond acceptors 5
TPSA 127.25 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 24
Fraction sp³ C 0.33
Formula C₁₅H₁₇N₃O₆

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 127.2
  • −1 ≤ LogP ≤ 5 -0.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.3
  • LogP ≤ 5 -0.08
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 127.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN1CCN(C(=O)N[C@H](C(=O)O)c2ccc(O)cc2)C(=O)C1=O
InChI 
InChI=1S/C15H17N3O6/c1-2-17-7-8-18(13(21)12(17)20)15(24)16-11(14(22)23)9-3-5-10(19)6-4-9/h3-6,11,19H,2,7-8H2,1H3,(H,16,24)(H,22,23)/t11-/m0/s1
InChIKey 
IPARGUVYMOMVNU-NSHDSACASA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
59J
Homolog
Q51504

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 25

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 49

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

Compound Similarity (Tanimoto)