Ligand profile

5WP

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

Bound to: VK055_0297 — phosphoenolpyruvate synthase

Via homolog PDB 5fbu UniProt A0A0X1KHF9 Formula C₄₃H₆₉N₄O₁₄P
Mol. weight 897.01 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5WP
PDB
5fbu
UniProt (similar protein)
A0A0X1KHF9
Target protein
VK055_0297

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 897.01 Da
LogP (Crippen) 4.39
H-bond donors 9
H-bond acceptors 15
TPSA 252.44 Ų
Rotatable bonds 10
Aromatic rings 2 / 5
Heavy atoms 62
Fraction sp³ C 0.65
Formula C₄₃H₆₉N₄O₁₄P

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 252.4
  • −1 ≤ LogP ≤ 5 4.39
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 897.0
  • LogP ≤ 5 4.39
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 252.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOc1c(c(c2c3c1[C@@H](O/C=C/[C@@H]([C@H]([C@H]([C@H]([C@@H]([C@H]([C@H]([C@@H](/C=C/C[C@@H](C(=O)Nc(c2O)c(c3)CNN4CCN(CC4)C)C)C)OP(=O)(O)O)C)O)C)O[C@@H](C)O)C)OC)O)O)C
InChI 
InChI=1S/C43H69N4O14P/c1-11-58-41-28(7)37(50)33-31-21-30(22-44-47-18-16-46(9)17-19-47)35(38(33)51)45-42(52)24(3)14-12-13-23(2)39(61-62(54,55)56)26(5)36(49)27(6)40(60-29(8)48)25(4)32(57-10)15-20-59-43(53)34(31)41/h12-13,15,20-21,23-27,29,32,36,39-40,43-44,48-51,53H,11,14,16-19,22H2,1-10H3,(H,45,52)(H2,54,55,56)/b13-12+,20-15+/t23-,24+,25-,26-,27+,29+,32+,36-,39+,40-,43-/m1/s1
InChIKey 
BCZNICVDDJLKHF-XVSBWFCFSA-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
PF00391

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_0297.

PDB 6

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)