Ligand profile

JYD

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

Bound to: KP13_05015 — Fumarate hydratase class I, aerobic

Via homolog PDB 6msn UniProt E9AE57 Formula C₄H₆O₄S
Mol. weight 150.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JYD
PDB
6msn
UniProt (similar protein)
E9AE57
Target protein
KP13_05015

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 150.16 Da
LogP (Crippen) -0.16
H-bond donors 3
H-bond acceptors 3
TPSA 74.60 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.50
Formula C₄H₆O₄S

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 74.6
  • −1 ≤ LogP ≤ 5 -0.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 150.2
  • LogP ≤ 5 -0.16
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H](C(=O)O)S)C(=O)O
InChI 
InChI=1S/C4H6O4S/c5-3(6)1-2(9)4(7)8/h2,9H,1H2,(H,5,6)(H,7,8)/t2-/m0/s1
InChIKey 
NJRXVEJTAYWCQJ-REOHCLBHSA-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
PF05681' 'PF05683

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_05015.

PDB 5

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

Ligand PDB entry

ZINC 41

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

Compound Similarity (Tanimoto)