Ligand profile

DHD

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

Bound to: KP13_00570 — Cystathionine gamma-synthase

Via homolog PDB 1cs1 UniProt P00935 Formula C₅H₄O₆
Mol. weight 160.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DHD
PDB
1cs1
UniProt (similar protein)
P00935
Target protein
KP13_00570

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 160.08 Da
LogP (Crippen) -1.32
H-bond donors 2
H-bond acceptors 4
TPSA 108.74 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.20
Formula C₅H₄O₆

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 108.7
  • −1 ≤ LogP ≤ 5 -1.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 160.1
  • LogP ≤ 5 -1.32
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 108.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)C(=O)O)C(=O)C(=O)O
InChI 
InChI=1S/C5H4O6/c6-2(4(8)9)1-3(7)5(10)11/h1H2,(H,8,9)(H,10,11)
InChIKey 
TVKBBTQJNQDZRU-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF01053

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_00570.

PDB 6

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 25

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

Compound Similarity (Tanimoto)