Ligand profile

DBK

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

Bound to: VK055_1741 — HAD ATPase, P-type, IC family protein

Via homolog PDB 3nal UniProt B6CAM1 Formula C₃₄H₅₂O₁₀
Mol. weight 620.78 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DBK
PDB
3nal
UniProt (similar protein)
B6CAM1
Target protein
VK055_1741

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 620.78 Da
LogP (Crippen) 5.17
H-bond donors 2
H-bond acceptors 10
TPSA 145.66 Ų
Rotatable bonds 14
Aromatic rings 0 / 3
Heavy atoms 44
Fraction sp³ C 0.76
Formula C₃₄H₅₂O₁₀

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 145.7
  • −1 ≤ LogP ≤ 5 5.17
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 620.8
  • LogP ≤ 5 5.17
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 145.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCC(=O)O[C@H]1C[C@]([C@H]2C[C@H](C(=C2[C@H]3[C@]1([C@](C(=O)O3)(C)O)O)C)OC(=O)/C(=C\C)/C)(C)OC(=O)C
InChI 
InChI=1S/C34H52O10/c1-8-10-11-12-13-14-15-16-17-18-27(36)42-26-20-32(6,44-23(5)35)24-19-25(41-30(37)21(3)9-2)22(4)28(24)29-34(26,40)33(7,39)31(38)43-29/h9,24-26,29,39-40H,8,10-20H2,1-7H3/b21-9-/t24-,25+,26-,29-,32-,33+,34+/m0/s1
InChIKey 
PTOLDSROGFHZGU-VFCZBPRFSA-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
PF00122' 'PF00689

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_1741.

PDB 27

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)