Ligand profile

B5Y

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

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

Via homolog PDB 5wm5 UniProt A0A140DJY3 Formula C₁₈H₂₀N₅O₉P
Mol. weight 481.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B5Y
PDB
5wm5
UniProt (similar protein)
A0A140DJY3
Target protein
VK055_5117

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 481.36 Da
LogP (Crippen) 0.02
H-bond donors 5
H-bond acceptors 13
TPSA 212.37 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.33
Formula C₁₈H₂₀N₅O₉P

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 212.4
  • −1 ≤ LogP ≤ 5 0.02
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 481.4
  • LogP ≤ 5 0.02
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 212.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
InChI 
InChI=1S/C18H20N5O9P/c1-8-2-3-10(24)9(4-8)18(27)32-33(28,29)30-5-11-13(25)14(26)17(31-11)23-7-22-12-15(19)20-6-21-16(12)23/h2-4,6-7,11,13-14,17,24-26H,5H2,1H3,(H,28,29)(H2,19,20,21)/t11-,13+,14+,17+/m0/s1
InChIKey 
XBOIILKAIKTKFY-ZCTGUTNYSA-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)