Ligand profile

PFV

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 4l0l UniProt Q51504 Formula C₂₀H₂₆N₈O₁₂S₂
Mol. weight 634.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PFV
PDB
4l0l
UniProt (similar protein)
Q51504
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 634.61 Da
LogP (Crippen) -2.64
H-bond donors 9
H-bond acceptors 15
TPSA 313.96 Ų
Rotatable bonds 14
Aromatic rings 2 / 2
Heavy atoms 42
Fraction sp³ C 0.35
Formula C₂₀H₂₆N₈O₁₂S₂

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 314.0
  • −1 ≤ LogP ≤ 5 -2.64
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 634.6
  • LogP ≤ 5 -2.64
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 314.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O)[C@@H](CNC(=O)NCC2=CC(=O)C(=CN2O)O)NS(=O)(=O)O
InChI 
InChI=1S/C20H26N8O12S2/c1-20(2,17(33)34)40-26-15(12-8-41-18(21)25-12)16(32)24-11(7-29)10(27-42(37,38)39)5-23-19(35)22-4-9-3-13(30)14(31)6-28(9)36/h3,6-8,10-11,27,31,36H,4-5H2,1-2H3,(H2,21,25)(H,24,32)(H,33,34)(H2,22,23,35)(H,37,38,39)/b26-15-/t10-,11-/m1/s1
InChIKey 
DRGQACYRFXBYPT-SATPWBBZSA-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)