Ligand profile

ZDP

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

Bound to: VK055_3167 — diaminopimelate epimerase

Via homolog PDB 2gke UniProt P44859 Formula C₈H₁₆N₂O₄
Mol. weight 204.23 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZDP
PDB
2gke
UniProt (similar protein)
P44859
Target protein
VK055_3167

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 204.23 Da
LogP (Crippen) -0.63
H-bond donors 4
H-bond acceptors 4
TPSA 126.64 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.75
Formula C₈H₁₆N₂O₄

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 126.6
  • −1 ≤ LogP ≤ 5 -0.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 204.2
  • LogP ≤ 5 -0.63
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 126.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CCC[C@@H](C(=O)O)N)(C(=O)O)N
InChI 
InChI=1S/C8H16N2O4/c1-8(10,7(13)14)4-2-3-5(9)6(11)12/h5H,2-4,9-10H2,1H3,(H,11,12)(H,13,14)/t5-,8-/m0/s1
InChIKey 
TVZGBXIJPFGQBJ-XNCJUZBTSA-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
PF01678

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3167.

PDB 4

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

Ligand PDB entry

ZINC 37

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

Compound Similarity (Tanimoto)