Ligand profile

U3V

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

Bound to: VK055_2602 — ribosomal-protein-alanine acetyltransferase

Via homolog PDB 6wfg UniProt Q9GZZ1 Formula C₂₄H₃₈N₆O₄
Mol. weight 474.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U3V
PDB
6wfg
UniProt (similar protein)
Q9GZZ1
Target protein
VK055_2602

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 474.61 Da
LogP (Crippen) 0.86
H-bond donors 3
H-bond acceptors 6
TPSA 125.43 Ų
Rotatable bonds 6
Aromatic rings 1 / 3
Heavy atoms 34
Fraction sp³ C 0.71
Formula C₂₄H₃₈N₆O₄

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 125.4
  • −1 ≤ LogP ≤ 5 0.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 474.6
  • LogP ≤ 5 0.86
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 125.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)c1cc(n(n1)C)C(=O)N2CCC(CC2)C[C@@H](C(=O)NC)NC(=O)[C@@H]3CCCC(=O)N3
InChI 
InChI=1S/C24H38N6O4/c1-24(2,3)19-14-18(29(5)28-19)23(34)30-11-9-15(10-12-30)13-17(21(32)25-4)27-22(33)16-7-6-8-20(31)26-16/h14-17H,6-13H2,1-5H3,(H,25,32)(H,26,31)(H,27,33)/t16-,17-/m0/s1
InChIKey 
SLKUTPSFHQUWLD-IRXDYDNUSA-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)