Ligand profile

RB6

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

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog PDB 5tx9 UniProt A0A0H2WY27 Formula C₂₀H₂₄N₈O₆S₂
Mol. weight 536.60 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RB6
PDB
5tx9
UniProt (similar protein)
A0A0H2WY27
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 536.60 Da
LogP (Crippen) -1.50
H-bond donors 6
H-bond acceptors 13
TPSA 212.23 Ų
Rotatable bonds 9
Aromatic rings 1 / 4
Heavy atoms 36
Fraction sp³ C 0.45
Formula C₂₀H₂₄N₈O₆S₂

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 212.2
  • −1 ≤ LogP ≤ 5 -1.50
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 536.6
  • LogP ≤ 5 -1.50
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 212.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H](C=O)NC(=O)/C(=N\O)/c4nc(sn4)N)C(=O)O
InChI 
InChI=1S/C20H24N8O6S2/c21-20-25-15(27-36-20)14(26-34)16(30)23-12(7-29)17-24-13(19(32)33)10(8-35-17)5-9-2-4-28(18(9)31)11-1-3-22-6-11/h2,7,11-12,17,22,24,34H,1,3-6,8H2,(H,23,30)(H,32,33)(H2,21,25,27)/b26-14-/t11-,12-,17-/m1/s1
InChIKey 
MYAXGJQBOYOEHQ-SWBIIUODSA-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
PF00144' 'PF00768' 'PF09211

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)