Ligand profile

EA2

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

Bound to: VK055_4165 — isopentenyl-diphosphate delta-isomerase

Via homolog PDB 2i6k UniProt Q13907 Formula C₂H₉NO₇P₂
Mol. weight 221.04 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EA2
PDB
2i6k
UniProt (similar protein)
Q13907
Target protein
VK055_4165

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 221.04 Da
LogP (Crippen) -0.83
H-bond donors 4
H-bond acceptors 5
TPSA 139.31 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 1.00
Formula C₂H₉NO₇P₂

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 139.3
  • −1 ≤ LogP ≤ 5 -0.83
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 221.0
  • LogP ≤ 5 -0.83
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 139.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CO[P@@](=O)(O)OP(=O)(O)O)N
InChI 
InChI=1S/C2H9NO7P2/c3-1-2-9-12(7,8)10-11(4,5)6/h1-3H2,(H,7,8)(H2,4,5,6)
InChIKey 
VOBNSQKMDIOJTQ-UHFFFAOYSA-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
PF00293

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_4165.

PDB 7

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 7

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

Compound Similarity (Tanimoto)