Ligand profile

D1D

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

Bound to: KP13_31612 — Peptide methionine sulfoxide reductase msrA

Via homolog PDB 5fa9 UniProt Q73PT7 Formula C₄H₈O₂S₂
Mol. weight 152.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D1D
PDB
5fa9
UniProt (similar protein)
Q73PT7
Target protein
KP13_31612

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 152.24 Da
LogP (Crippen) 0.10
H-bond donors 2
H-bond acceptors 4
TPSA 40.46 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 8
Fraction sp³ C 1.00
Formula C₄H₈O₂S₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 40.5
  • −1 ≤ LogP ≤ 5 0.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 152.2
  • LogP ≤ 5 0.10
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@@H](CSS1)O)O
InChI 
InChI=1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m1/s1
InChIKey 
YPGMOWHXEQDBBV-QWWZWVQMSA-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
PF01625

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_31612.

PDB 5

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

Ligand PDB entry

ChEMBL 6

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)