Ligand profile

SD4

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

Bound to: KP13_04286 — Isoaspartyl peptidase

Via homolog PDB 4r4y UniProt Q47898 Formula C₄H₈N₂O₄
Mol. weight 148.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SD4
PDB
4r4y
UniProt (similar protein)
Q47898
Target protein
KP13_04286

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 148.12 Da
LogP (Crippen) -1.71
H-bond donors 4
H-bond acceptors 4
TPSA 112.65 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.50
Formula C₄H₈N₂O₄

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 112.6
  • −1 ≤ LogP ≤ 5 -1.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 148.1
  • LogP ≤ 5 -1.71
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 112.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H](C(=O)O)N)C(=O)NO
InChI 
InChI=1S/C4H8N2O4/c5-2(4(8)9)1-3(7)6-10/h2,10H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1
InChIKey 
ZBYVTTSIVDYQSO-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
PF01112

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_04286.

PDB 4

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

Ligand PDB entry

ChEMBL 5

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 46

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

Compound Similarity (Tanimoto)