Ligand profile

TOI

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

Bound to: VK055_4853 — 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylic-acid synthase

Via homolog PDB 5esu UniProt P9WK11 Formula C₂₆H₃₅N₄O₁₆P₂S⁺
Mol. weight 753.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TOI
PDB
5esu
UniProt (similar protein)
P9WK11
Target protein
VK055_4853

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 753.59 Da
LogP (Crippen) -0.04
H-bond donors 10
H-bond acceptors 13
TPSA 331.29 Ų
Rotatable bonds 17
Aromatic rings 2 / 3
Heavy atoms 49
Fraction sp³ C 0.46
Formula C₂₆H₃₅N₄O₁₆P₂S⁺

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 331.3
  • −1 ≤ LogP ≤ 5 -0.04
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 753.6
  • LogP ≤ 5 -0.04
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 17
  • TPSA ≤ 140 Ų 331.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C/1\C(=CNC(=N1)C)C[n+]2c(c(sc2[C@](CCC(=O)O)([C@H]3C=C[C@@H]([C@H]([C@@H]3C(=O)O)O)OC(=C)C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O)C
InChI 
InChI=1S/C26H34N4O16P2S/c1-12-18(7-9-44-48(42,43)46-47(39,40)41)49-25(30(12)11-15-10-28-14(3)29-22(15)27)26(38,8-6-19(31)32)16-4-5-17(45-13(2)23(34)35)21(33)20(16)24(36)37/h4-5,10,16-17,20-21,33,38H,2,6-9,11H2,1,3H3,(H7-,27,28,29,31,32,34,35,36,37,39,40,41,42,43)/p+1/t16-,17-,20+,21+,26-/m0/s1
InChIKey 
AJVZCJMDQDMTBE-BLORIJLWSA-O

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
PF02776

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_4853.

PDB 5

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

Ligand PDB entry

ChEMBL 2

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)