Ligand profile

IRC

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

Bound to: VK055_2674 — 2-hydroxyglutaryl-CoA dehydratase, D-component family protein

Via homolog PDB 3o3n UniProt Q5U923 Formula C₂₇H₄₆N₇O₁₈P₃S
Mol. weight 881.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IRC
PDB
3o3n
UniProt (similar protein)
Q5U923
Target protein
VK055_2674

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 881.69 Da
LogP (Crippen) -0.93
H-bond donors 10
H-bond acceptors 20
TPSA 383.86 Ų
Rotatable bonds 22
Aromatic rings 2 / 3
Heavy atoms 56
Fraction sp³ C 0.70
Formula C₂₇H₄₆N₇O₁₈P₃S

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 -0.93
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 881.7
  • LogP ≤ 5 -0.93
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 383.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O)O
InChI 
InChI=1S/C27H46N7O18P3S/c1-14(2)9-15(35)26(40)56-8-7-29-17(36)5-6-30-24(39)21(38)27(3,4)11-49-55(46,47)52-54(44,45)48-10-16-20(51-53(41,42)43)19(37)25(50-16)34-13-33-18-22(28)31-12-32-23(18)34/h12-16,19-21,25,35,37-38H,5-11H2,1-4H3,(H,29,36)(H,30,39)(H,44,45)(H,46,47)(H2,28,31,32)(H2,41,42,43)/t15-,16-,19-,20-,21+,25-/m1/s1
InChIKey 
CFNPCSNXESBNGR-LYALRYAQSA-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
PF06050

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_2674.

PDB 3

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

Ligand PDB entry

ZINC 4

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

Compound Similarity (Tanimoto)