Ligand profile

MXR

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

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog PDB 6ntz UniProt P0AEB2 Formula C₁₇H₂₇N₃O₅S
Mol. weight 385.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MXR
PDB
6ntz
UniProt (similar protein)
P0AEB2
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 385.49 Da
LogP (Crippen) -0.35
H-bond donors 3
H-bond acceptors 7
TPSA 119.30 Ų
Rotatable bonds 7
Aromatic rings 0 / 2
Heavy atoms 26
Fraction sp³ C 0.76
Formula C₁₇H₂₇N₃O₅S

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 119.3
  • −1 ≤ LogP ≤ 5 -0.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 385.5
  • LogP ≤ 5 -0.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 119.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=O)O)S[C@H]2C[C@@H](NC2)C(=O)N(C)C
InChI 
InChI=1S/C17H27N3O5S/c1-8-13(11(7-21)9(2)22)19-14(17(24)25)15(8)26-10-5-12(18-6-10)16(23)20(3)4/h7-13,15,18,22H,5-6H2,1-4H3,(H,24,25)/t8-,9-,10+,11-,12-,13-,15+/m1/s1
InChIKey 
UUIYVKJXUXGPKB-DKLFCYGSSA-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
PF00768

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_1655.

PDB 13

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

Ligand PDB entry

ChEMBL 1

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)