Ligand profile

SKM

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

Bound to: VK055_3791 — dehydroshikimate reductase

Via homolog PDB 2hk9 UniProt O67049 Formula C₇H₁₀O₅
Mol. weight 174.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SKM
PDB
2hk9
UniProt (similar protein)
O67049
Target protein
VK055_3791

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 174.15 Da
LogP (Crippen) -1.52
H-bond donors 4
H-bond acceptors 4
TPSA 97.99 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 12
Fraction sp³ C 0.57
Formula C₇H₁₀O₅

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 98.0
  • −1 ≤ LogP ≤ 5 -1.52
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 174.2
  • LogP ≤ 5 -1.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 98.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
InChI 
InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
InChIKey 
JXOHGGNKMLTUBP-HSUXUTPPSA-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
PF01488' 'PF08501' 'PF18317

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_3791.

PDB 3

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)