Ligand profile

DPU

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

Bound to: VK055_1728 — dethiobiotin synthase

Via homolog PDB 1dak UniProt P13000 Formula C₁₀H₂₁N₂O₇P
Mol. weight 312.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DPU
PDB
1dak
UniProt (similar protein)
P13000
Target protein
VK055_1728

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 312.26 Da
LogP (Crippen) 0.56
H-bond donors 5
H-bond acceptors 5
TPSA 159.18 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.80
Formula C₁₀H₂₁N₂O₇P

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 159.2
  • −1 ≤ LogP ≤ 5 0.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 312.3
  • LogP ≤ 5 0.56
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 159.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)OP(=O)(O)O)N
InChI 
InChI=1S/C10H21N2O7P/c1-7(11)8(5-3-2-4-6-9(13)14)12-10(15)19-20(16,17)18/h7-8H,2-6,11H2,1H3,(H,12,15)(H,13,14)(H2,16,17,18)/t7-,8+/m0/s1
InChIKey 
UJJZZEABROBUCE-JGVFFNPUSA-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
PF01656

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_1728.

PDB 8

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)