Ligand profile

DTB

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

Bound to: VK055_1728 — dethiobiotin synthase

Via homolog PDB 1dam UniProt P13000 Formula C₁₀H₁₈N₂O₃
Mol. weight 214.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DTB
PDB
1dam
UniProt (similar protein)
P13000
Target protein
VK055_1728

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 214.26 Da
LogP (Crippen) 1.09
H-bond donors 3
H-bond acceptors 2
TPSA 78.43 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 15
Fraction sp³ C 0.80
Formula C₁₀H₁₈N₂O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 78.4
  • −1 ≤ LogP ≤ 5 1.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 214.3
  • LogP ≤ 5 1.09
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 78.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@H](NC(=O)N1)CCCCCC(=O)O
InChI 
InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)/t7-,8+/m0/s1
InChIKey 
AUTOLBMXDDTRRT-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)