Ligand profile

CMX

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

Bound to: VK055_1802 — citrate (Si)-synthase

Via homolog PDB 2h12 UniProt P20901 Formula C₂₃H₃₈N₇O₁₈P₃
Mol. weight 793.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CMX
PDB
2h12
UniProt (similar protein)
P20901
Target protein
VK055_1802

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 793.51 Da
LogP (Crippen) -1.73
H-bond donors 10
H-bond acceptors 18
TPSA 383.86 Ų
Rotatable bonds 20
Aromatic rings 2 / 3
Heavy atoms 51
Fraction sp³ C 0.65
Formula C₂₃H₃₈N₇O₁₈P₃

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 383.9
  • −1 ≤ LogP ≤ 5 -1.73
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 793.5
  • LogP ≤ 5 -1.73
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • TPSA ≤ 140 Ų 383.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCCC(=O)O)O
InChI 
InChI=1S/C23H38N7O18P3/c1-23(2,18(35)21(36)26-7-5-13(31)25-6-3-4-14(32)33)9-45-51(42,43)48-50(40,41)44-8-12-17(47-49(37,38)39)16(34)22(46-12)30-11-29-15-19(24)27-10-28-20(15)30/h10-12,16-18,22,34-35H,3-9H2,1-2H3,(H,25,31)(H,26,36)(H,32,33)(H,40,41)(H,42,43)(H2,24,27,28)(H2,37,38,39)/t12-,16-,17-,18+,22-/m1/s1
InChIKey 
SKRDARVCOPFVCP-GRFIIANRSA-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
PF00285

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_1802.

PDB 3

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)