Ligand profile

COD

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

Bound to: VK055_0526 — S-(hydroxymethyl)glutathione dehydrogenase/classIII alcohol dehydrogenase

Via homolog PDB 6cxx UniProt P00327 Formula C₂₁H₃₅N₇O₁₃P₂S
Mol. weight 687.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
COD
PDB
6cxx
UniProt (similar protein)
P00327
Target protein
VK055_0526

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 687.56 Da
LogP (Crippen) -1.78
H-bond donors 9
H-bond acceptors 17
TPSA 300.03 Ų
Rotatable bonds 16
Aromatic rings 2 / 3
Heavy atoms 44
Fraction sp³ C 0.67
Formula C₂₁H₃₅N₇O₁₃P₂S

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 300.0
  • −1 ≤ LogP ≤ 5 -1.78
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 687.6
  • LogP ≤ 5 -1.78
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 300.0
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)O)[C@H](C(=O)NCCC(=O)NCCS)O
InChI 
InChI=1S/C21H35N7O13P2S/c1-21(2,16(32)19(33)24-4-3-12(29)23-5-6-44)8-39-43(36,37)41-42(34,35)38-7-11-14(30)15(31)20(40-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-32,44H,3-8H2,1-2H3,(H,23,29)(H,24,33)(H,34,35)(H,36,37)(H2,22,25,26)/t11-,14-,15-,16+,20-/m1/s1
InChIKey 
KDTSHFARGAKYJN-IBOSZNHHSA-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
PF00107' 'PF08240

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_0526.

PDB 26

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

Ligand PDB entry

ChEMBL 16

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)