Ligand profile

7D9

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

Bound to: VK055_4419 — phenolic acid decarboxylase subunit C

Via homolog PDB 5m1e UniProt P0AAB5 Formula C₂₂H₃₁N₄O₁₂PS
Mol. weight 606.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7D9
PDB
5m1e
UniProt (similar protein)
P0AAB5
Target protein
VK055_4419

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 606.55 Da
LogP (Crippen) -0.64
H-bond donors 8
H-bond acceptors 11
TPSA 254.02 Ų
Rotatable bonds 8
Aromatic rings 2 / 4
Heavy atoms 40
Fraction sp³ C 0.55
Formula C₂₂H₃₁N₄O₁₂PS

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 254.0
  • −1 ≤ LogP ≤ 5 -0.64
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 606.5
  • LogP ≤ 5 -0.64
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 254.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)NC(=O)NC4=O)S(=O)(=O)O)(C)C
InChI 
InChI=1S/C22H31N4O12PS/c1-9-5-11-16-15(10(9)2)22(3,4)6-14(40(35,36)37)26(16)17-19(23-21(31)24-20(17)30)25(11)7-12(27)18(29)13(28)8-38-39(32,33)34/h5,12-14,18,27-29H,6-8H2,1-4H3,(H2,32,33,34)(H,35,36,37)(H2,23,24,30,31)/t12-,13+,14+,18-/m0/s1
InChIKey 
TZDQUUMSMXVHAK-LWGWVAHUSA-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
PF01977

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_4419.

PDB 2

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

Ligand PDB entry

ZINC 37

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

Compound Similarity (Tanimoto)