Ligand profile

CHEMBL2107817

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_0673 — penicillin-binding protein 2

Via homolog UniProt P0AD65 Formula C₇H₁₀N₃NaO₆S
pchembl 6.23 ~588.8 nM
Mol. weight 287.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL2107817
UniProt (similar protein)
P0AD65
pchembl
6.230 (~588.8 nM)
Target protein
VK055_0673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 287.23 Da
LogP (Crippen) -4.86
H-bond donors 1
H-bond acceptors 6
TPSA 133.07 Ų
Rotatable bonds 3
Aromatic rings 0 / 2
Heavy atoms 18
Fraction sp³ C 0.71
Formula C₇H₁₀N₃NaO₆S

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 133.1
  • −1 ≤ LogP ≤ 5 -4.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 287.2
  • LogP ≤ 5 -4.86
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 133.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC(=O)[C@@H]1CC[C@@H]2CN1C(=O)N2OS(=O)(=O)[O-].[Na+]
InChI 
InChI=1S/C7H11N3O6S.Na/c8-6(11)5-2-1-4-3-9(5)7(12)10(4)16-17(13,14)15;/h4-5H,1-3H2,(H2,8,11)(H,13,14,15);/q;+1/p-1/t4-,5+;/m1./s1
InChIKey 
RTCIKUMODPANKX-JBUOLDKXSA-M

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
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_0673.

PDB 4

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

Ligand PDB entry

ChEMBL 5

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)