Ligand profile

9VH

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

Bound to: KP13_00143 — Alpha-xylosidase

Via homolog PDB 6pnr UniProt C4ZGB7 Formula C₆H₁₃NO₅S
Mol. weight 211.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9VH
PDB
6pnr
UniProt (similar protein)
C4ZGB7
Target protein
KP13_00143

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 211.24 Da
LogP (Crippen) -2.18
H-bond donors 4
H-bond acceptors 5
TPSA 106.86 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 13
Fraction sp³ C 1.00
Formula C₆H₁₃NO₅S

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 106.9
  • −1 ≤ LogP ≤ 5 -2.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 211.2
  • LogP ≤ 5 -2.18
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 106.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H](CN1)O)O)CS(=O)(=O)O
InChI 
InChI=1S/C6H13NO5S/c8-5-2-7-1-4(6(5)9)3-13(10,11)12/h4-9H,1-3H2,(H,10,11,12)/t4-,5-,6-/m1/s1
InChIKey 
RCSXCFCCYYFFCY-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
PF01055

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00143.

PDB 9

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)