Ligand profile

ADJ

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

Bound to: VK055_1230 — nadE

Via homolog PDB 1kqp UniProt P08164 Formula C₃₁H₄₄N₁₁O₂₁P₃
Mol. weight 999.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ADJ
PDB
1kqp
UniProt (similar protein)
P08164
Target protein
VK055_1230

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 999.67 Da
LogP (Crippen) -4.15
H-bond donors 12
H-bond acceptors 29
TPSA 469.83 Ų
Rotatable bonds 17
Aromatic rings 4 / 8
Heavy atoms 66
Fraction sp³ C 0.61
Formula C₃₁H₄₄N₁₁O₂₁P₃

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 469.8
  • −1 ≤ LogP ≤ 5 -4.15
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 999.7
  • LogP ≤ 5 -4.15
  • H-bond donors ≤ 5 12
  • H-bond acceptors ≤ 10 29
Veber's rules Fail
  • Rotatable bonds ≤ 10 17
  • TPSA ≤ 140 Ų 469.8
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)OC(C4=CCCN(C4)[C@H]5[C@@H]([C@@H]([C@H](O5)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]6[C@H]([C@H]([C@@H](O6)n7cnc8c7ncnc8N)O)O)O)O)O)O)O)N
InChI 
InChI=1S/C31H44N11O21P3/c32-24-16-26(36-8-34-24)41(10-38-16)29-22(47)19(44)14(60-29)5-56-64(50,51)62-31(49)12-2-1-3-40(4-12)28-21(46)18(43)13(59-28)6-57-65(52,53)63-66(54,55)58-7-15-20(45)23(48)30(61-15)42-11-39-17-25(33)35-9-37-27(17)42/h2,8-11,13-15,18-23,28-31,43-49H,1,3-7H2,(H,50,51)(H,52,53)(H,54,55)(H2,32,34,36)(H2,33,35,37)/t13-,14-,15-,18-,19-,20-,21-,22-,23-,28-,29-,30-,31?/m1/s1
InChIKey 
DBSVVYFUZBLHSN-JFLYKPBPSA-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
PF02540

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_1230.

PDB 4

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)