Ligand profile

J2J

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

Bound to: VK055_5117 — 2,3-dihydroxybenzoate-AMP ligase

Via homolog PDB 6e97 UniProt Q47NR5 Formula C₁₇H₁₈N₅O₁₀P
Mol. weight 483.33 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
J2J
PDB
6e97
UniProt (similar protein)
Q47NR5
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.33 Da
LogP (Crippen) -0.59
H-bond donors 6
H-bond acceptors 14
TPSA 232.60 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.29
Formula C₁₇H₁₈N₅O₁₀P

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 232.6
  • −1 ≤ LogP ≤ 5 -0.59
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 483.3
  • LogP ≤ 5 -0.59
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 232.6
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c(c(c1)O)O)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
InChI 
InChI=1S/C17H18N5O10P/c18-14-10-15(20-5-19-14)22(6-21-10)16-13(26)12(25)9(31-16)4-30-33(28,29)32-17(27)7-2-1-3-8(23)11(7)24/h1-3,5-6,9,12-13,16,23-26H,4H2,(H,28,29)(H2,18,19,20)/t9-,12-,13-,16-/m1/s1
InChIKey 
ULPVJDOMCRTJSN-RVXWVPLUSA-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
PF00501

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_5117.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 82

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)