Ligand profile

9TN

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

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

Via homolog PDB 2yfy UniProt P04191-2 Formula C₃₀H₄₄O₁₁
Mol. weight 580.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9TN
PDB
2yfy
UniProt (similar protein)
P04191-2
Target protein
VK055_1741

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 580.67 Da
LogP (Crippen) 2.58
H-bond donors 3
H-bond acceptors 11
TPSA 165.89 Ų
Rotatable bonds 10
Aromatic rings 0 / 3
Heavy atoms 41
Fraction sp³ C 0.73
Formula C₃₀H₄₄O₁₁

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 165.9
  • −1 ≤ LogP ≤ 5 2.58
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 580.7
  • LogP ≤ 5 2.58
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 165.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCC(=O)O[C@H]1[C@H]2C(=C([C@@H]1OC(=O)/C(=C/C)/C)C)[C@H]3[C@]([C@H](C[C@]2(C)OC(=O)C)O)([C@](C(=O)O3)(C)O)O
InChI 
InChI=1S/C30H44O11/c1-8-10-11-12-13-14-20(33)38-24-22-21(17(4)23(24)39-26(34)16(3)9-2)25-30(37,29(7,36)27(35)40-25)19(32)15-28(22,6)41-18(5)31/h9,19,22-25,32,36-37H,8,10-15H2,1-7H3/b16-9+/t19-,22+,23-,24-,25-,28-,29+,30+/m0/s1
InChIKey 
UBPDDZPGODTCDF-NPAVTDDVSA-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)