Ligand profile

CHEMBL520642

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5052 — DD-carboxypeptidase, penicillin-binding protein 6b

Via homolog UniProt A0A0H2WY27 Formula C₂₀H₂₂N₈O₆S₂

Mol. weight 534.58 Da

Permeability Check

PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID: CHEMBL520642
UniProt (similar protein): A0A0H2WY27
Target protein: VK055_5052

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 534.58 Da

LogP (Crippen) -1.44

H-bond donors 5

H-bond acceptors 12

TPSA 203.44 Å²

Rotatable bonds 6

Aromatic rings 1 / 5

Heavy atoms 36

Fraction sp³ C 0.45

Formula C₂₀H₂₂N₈O₆S₂

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 Å² and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

TPSA ≤ 90 Å² 203.4
−1 ≤ LogP ≤ 5 -1.44

Lipinski's Rule of Five Fail 2 violations

MW ≤ 500 Da 534.6
LogP ≤ 5 -1.44
H-bond donors ≤ 5 5
H-bond acceptors ≤ 10 12

Veber's rules Fail

Rotatable bonds ≤ 10 6
TPSA ≤ 140 Å² 203.4

PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES

Nc1nc(/C(=N/O)C(=O)N[C@@H]2C(=O)N3C(C(=O)O)=C(/C=C4\CCN([C@@H]5CCNC5)C4=O)CS[C@H]23)ns1

InChI

InChI=1S/C20H22N8O6S2/c21-20-24-14(26-36-20)11(25-34)15(29)23-12-17(31)28-13(19(32)33)9(7-35-18(12)28)5-8-2-4-27(16(8)30)10-1-3-22-6-10/h5,10,12,18,22,34H,1-4,6-7H2,(H,23,29)(H,32,33)(H2,21,24,26)/b8-5+,25-11-/t10-,12-,18-/m1/s1

InChIKey

VOAZJEPQLGBXGO-SDAWRPRTSA-N

Provenance

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

Method: LigQ nearest_k
Source: ChEMBL
Activity: Active
Curation: pdb_similarity_tanimoto
Binding sites: PF00768' 'PF09211

External resources

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

ChEMBL ChEMBL compound CHEMBL520642 →
UniProt UniProt A0A0H2WY27 (homolog) →
PubChem PubChem (by InChIKey) →
Cheminformatics SwissADME prediction →
Cheminformatics SwissTargetPrediction →
Web Google Scholar (search “CHEMBL520642”) →

Other ligands for this protein

Quick navigation to other ligands bound to VK055_5052.

PDB 14

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)