Ligand profile

DL5

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

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

Via homolog PDB 5a3q UniProt P04191-2 Formula C₁₇H₁₉N₈O₁₈P₃
Mol. weight 716.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DL5
PDB
5a3q
UniProt (similar protein)
P04191-2
Target protein
VK055_1741

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 716.30 Da
LogP (Crippen) -1.08
H-bond donors 6
H-bond acceptors 19
TPSA 380.48 Ų
Rotatable bonds 10
Aromatic rings 2 / 5
Heavy atoms 46
Fraction sp³ C 0.41
Formula C₁₇H₁₉N₈O₁₈P₃

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 380.5
  • −1 ≤ LogP ≤ 5 -1.08
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 716.3
  • LogP ≤ 5 -1.08
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 380.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N
InChI 
InChI=1S/C17H19N8O18P3/c18-14-11-15(20-4-19-14)22(5-21-11)16-13-12(8(40-16)3-39-46(37,38)43-45(35,36)6-44(32,33)34)41-17(42-13)9(24(28)29)1-7(23(26)27)2-10(17)25(30)31/h1-2,4-5,8,12-13,16H,3,6H2,(H,26,27)(H,35,36)(H,37,38)(H2,18,19,20)(H2,32,33,34)/t8-,12-,13-,16-/m1/s1
InChIKey 
WOUJMFLAWZHYLK-KWDXPJCYSA-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' 'PF00702' 'PF13246

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)