Ligand profile

HD2

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

Bound to: VK055_0681 — alpha/beta hydrolase fold family protein

Via homolog PDB 5alu UniProt P34913 Formula C₂₄H₃₄N₄O₃
Mol. weight 426.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HD2
PDB
5alu
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.56 Da
LogP (Crippen) 3.00
H-bond donors 3
H-bond acceptors 6
TPSA 96.37 Ų
Rotatable bonds 5
Aromatic rings 1 / 7
Heavy atoms 31
Fraction sp³ C 0.79
Formula C₂₄H₃₄N₄O₃

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 96.4
  • −1 ≤ LogP ≤ 5 3.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.6
  • LogP ≤ 5 3.00
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 96.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(nc(n1)N[C@H]2CCOC2)C3CCCC3)C(=O)NC4[C@@H]5CC6C[C@H]4CC(C5)(C6)O
InChI 
InChI=1S/C24H34N4O3/c29-22(27-20-16-7-14-8-17(20)11-24(30,9-14)10-16)19-12-25-23(26-18-5-6-31-13-18)28-21(19)15-3-1-2-4-15/h12,14-18,20,30H,1-11,13H2,(H,27,29)(H,25,26,28)/t14?,16-,17+,18-,20?,24?/m0/s1
InChIKey 
VMTZDIHMLVWUQZ-XANBXHNASA-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
PF00561' 'PF00702

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_0681.

PDB 98

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

Ligand PDB entry

ChEMBL 100

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)