Ligand profile

NDE

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

Bound to: VK055_3518 — gpsA

Via homolog PDB 1n1e UniProt P90551 Formula C₂₄H₃₂N₇O₂₀P₃
Mol. weight 831.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NDE
PDB
1n1e
UniProt (similar protein)
P90551
Target protein
VK055_3518

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 831.47 Da
LogP (Crippen) -4.94
H-bond donors 10
H-bond acceptors 22
TPSA 425.15 Ų
Rotatable bonds 16
Aromatic rings 3 / 5
Heavy atoms 54
Fraction sp³ C 0.50
Formula C₂₄H₃₂N₇O₂₀P₃

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 425.2
  • −1 ≤ LogP ≤ 5 -4.94
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 831.5
  • LogP ≤ 5 -4.94
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 22
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 425.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c[n+](cc(c1[C@H](C(=O)COP(=O)(O)O)O)C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O
InChI 
InChI=1S/C24H32N7O20P3/c25-20-14-22(28-7-27-20)31(8-29-14)24-19(37)17(35)13(50-24)6-48-54(44,45)51-53(42,43)47-5-12-16(34)18(36)23(49-12)30-2-1-9(10(3-30)21(26)38)15(33)11(32)4-46-52(39,40)41/h1-3,7-8,12-13,15-19,23-24,33-37H,4-6H2,(H7-,25,26,27,28,38,39,40,41,42,43,44,45)/t12-,13-,15-,16-,17-,18-,19-,23-,24-/m1/s1
InChIKey 
IVZPTIKSOMOSEU-IATPXFKGSA-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
PF01210' 'PF07479

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_3518.

PDB 11

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)