Ligand profile

59J

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 5df9 UniProt Q51504 Formula C₂₃H₂₇N₅O₉S
Mol. weight 549.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
59J
PDB
5df9
UniProt (similar protein)
Q51504
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 549.56 Da
LogP (Crippen) -0.36
H-bond donors 5
H-bond acceptors 9
TPSA 206.01 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 38
Fraction sp³ C 0.43
Formula C₂₃H₂₇N₅O₉S

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 206.0
  • −1 ≤ LogP ≤ 5 -0.36
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 549.6
  • LogP ≤ 5 -0.36
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 206.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)N[C@@H]([C@@H]3N=C([C@H](CS3)C)C(=O)O)C(=O)O
InChI 
InChI=1S/C23H27N5O9S/c1-3-27-8-9-28(20(32)19(27)31)23(37)26-15(12-4-6-13(29)7-5-12)17(30)24-16(22(35)36)18-25-14(21(33)34)11(2)10-38-18/h4-7,11,15-16,18,29H,3,8-10H2,1-2H3,(H,24,30)(H,26,37)(H,33,34)(H,35,36)/t11-,15+,16-,18+/m0/s1
InChIKey 
YNTRKCUUJNUMAH-QOQPWIFLSA-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)