Ligand profile

59H

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

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog PDB 5df7 UniProt Q51504 Formula C₂₀H₂₅N₅O₆S
Mol. weight 463.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
59H
PDB
5df7
UniProt (similar protein)
Q51504
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 463.52 Da
LogP (Crippen) 0.04
H-bond donors 5
H-bond acceptors 7
TPSA 156.94 Ų
Rotatable bonds 7
Aromatic rings 1 / 3
Heavy atoms 32
Fraction sp³ C 0.45
Formula C₂₀H₂₅N₅O₆S

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 156.9
  • −1 ≤ LogP ≤ 5 0.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 463.5
  • LogP ≤ 5 0.04
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 156.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2ccccc2)NC(=O)N3CCNC3=O)C(=O)O)C
InChI 
InChI=1S/C20H25N5O6S/c1-20(2)14(17(28)29)24-16(32-20)12(10-26)22-15(27)13(11-6-4-3-5-7-11)23-19(31)25-9-8-21-18(25)30/h3-7,10,12-14,16,24H,8-9H2,1-2H3,(H,21,30)(H,22,27)(H,23,31)(H,28,29)/t12-,13-,14+,16-/m1/s1
InChIKey 
FATONWNMDXFMAN-HGTKMLMNSA-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)