Ligand profile

JPP

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 4kqo UniProt G3XD46 Formula C₂₃H₂₉N₅O₇S
Mol. weight 519.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JPP
PDB
4kqo
UniProt (similar protein)
G3XD46
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 519.58 Da
LogP (Crippen) -0.29
H-bond donors 4
H-bond acceptors 8
TPSA 165.22 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 36
Fraction sp³ C 0.48
Formula C₂₃H₂₉N₅O₇S

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 165.2
  • −1 ≤ LogP ≤ 5 -0.29
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 519.6
  • LogP ≤ 5 -0.29
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 165.2
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](c2ccccc2)C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O
InChI 
InChI=1S/C23H29N5O7S/c1-4-27-10-11-28(20(32)19(27)31)22(35)25-15(13-8-6-5-7-9-13)17(30)24-14(12-29)18-26-16(21(33)34)23(2,3)36-18/h5-9,12,14-16,18,26H,4,10-11H2,1-3H3,(H,24,30)(H,25,35)(H,33,34)/t14-,15-,16+,18-/m1/s1
InChIKey 
CJYMHKMECTVNSA-XLMAVXFVSA-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)