Ligand profile

IMB

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

Bound to: VK055_2379 — 1-deoxy-D-xylulose 5-phosphate reductoisomerase

Via homolog PDB 1t1r UniProt P45568 Formula C₁₀H₁₂N₂O₆P₂
Mol. weight 318.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IMB
PDB
1t1r
UniProt (similar protein)
P45568
Target protein
VK055_2379

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 318.16 Da
LogP (Crippen) 1.29
H-bond donors 5
H-bond acceptors 4
TPSA 139.98 Ų
Rotatable bonds 4
Aromatic rings 2 / 2
Heavy atoms 20
Fraction sp³ C 0.10
Formula C₁₀H₁₂N₂O₆P₂

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 140.0
  • −1 ≤ LogP ≤ 5 1.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 318.2
  • LogP ≤ 5 1.29
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 140.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)ccnc2NC(P(=O)(O)O)P(=O)(O)O
InChI 
InChI=1S/C10H12N2O6P2/c13-19(14,15)10(20(16,17)18)12-9-8-4-2-1-3-7(8)5-6-11-9/h1-6,10H,(H,11,12)(H2,13,14,15)(H2,16,17,18)
InChIKey 
JPVMIOWESIQIGB-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
PF02670' 'PF08436' 'PF13288

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_2379.

PDB 6

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

Ligand PDB entry

ChEMBL 42

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)