Ligand profile

NA7

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

Bound to: VK055_4042 — 2,5-diketo-D-gluconic acid reductase A

Via homolog PDB 2wzm UniProt A0QV09 Formula C₁₅H₂₄N₅O₁₆P₃
Mol. weight 623.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NA7
PDB
2wzm
UniProt (similar protein)
A0QV09
Target protein
VK055_4042

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 623.30 Da
LogP (Crippen) -2.48
H-bond donors 8
H-bond acceptors 17
TPSA 317.82 Ų
Rotatable bonds 11
Aromatic rings 2 / 4
Heavy atoms 39
Fraction sp³ C 0.67
Formula C₁₅H₂₄N₅O₁₆P₃

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 317.8
  • −1 ≤ LogP ≤ 5 -2.48
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 623.3
  • LogP ≤ 5 -2.48
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 317.8
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]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H](CO4)O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C15H24N5O16P3/c16-13-9-14(18-4-17-13)20(5-19-9)15-12(35-37(24,25)26)11(23)8(34-15)3-33-39(29,30)36-38(27,28)32-2-7-10(22)6(21)1-31-7/h4-8,10-12,15,21-23H,1-3H2,(H,27,28)(H,29,30)(H2,16,17,18)(H2,24,25,26)/t6-,7+,8+,10-,11+,12+,15+/m0/s1
InChIKey 
XDDBFIXGEVGCEU-AOOZFPJJSA-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
PF00248

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_4042.

PDB 1

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)