Ligand profile

U3Y

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

Bound to: VK055_2602 — ribosomal-protein-alanine acetyltransferase

Via homolog PDB 6wfo UniProt Q9GZZ1 Formula C₂₃H₂₄N₁₀O₅S
Mol. weight 552.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U3Y
PDB
6wfo
UniProt (similar protein)
Q9GZZ1
Target protein
VK055_2602

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 552.58 Da
LogP (Crippen) -0.30
H-bond donors 4
H-bond acceptors 10
TPSA 195.27 Ų
Rotatable bonds 6
Aromatic rings 3 / 5
Heavy atoms 39
Fraction sp³ C 0.35
Formula C₂₃H₂₄N₁₀O₅S

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 195.3
  • −1 ≤ LogP ≤ 5 -0.30
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 552.6
  • LogP ≤ 5 -0.30
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 195.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNC(=O)c1csc(n1)[C@H]2C[C@@H](CN2C(=O)c3ccc(cc3)c4[nH]nnn4)NC(=O)[C@@H]5CC(=O)N(C(=O)N5)C
InChI 
InChI=1S/C23H24N10O5S/c1-24-19(35)15-10-39-21(26-15)16-7-13(25-20(36)14-8-17(34)32(2)23(38)27-14)9-33(16)22(37)12-5-3-11(4-6-12)18-28-30-31-29-18/h3-6,10,13-14,16H,7-9H2,1-2H3,(H,24,35)(H,25,36)(H,27,38)(H,28,29,30,31)/t13-,14-,16+/m0/s1
InChIKey 
SYFLGRBSBZONAM-OFQRWUPVSA-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
PF00583

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_2602.

PDB 5

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 10

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)