Ligand profile

SYD

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P45568 Formula C₁₂H₁₂NO₃P
pchembl 6.08 ~831.8 nM
Mol. weight 249.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SYD
UniProt (similar protein)
P45568
pchembl
6.080 (~831.8 nM)
Target protein
VK055_2379

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 249.21 Da
LogP (Crippen) 2.43
H-bond donors 2
H-bond acceptors 2
TPSA 70.42 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 17
Fraction sp³ C 0.08
Formula C₁₂H₁₂NO₃P

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 70.4
  • −1 ≤ LogP ≤ 5 2.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 249.2
  • LogP ≤ 5 2.43
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 70.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)c2ccc(nc2)CP(=O)(O)O
InChI 
InChI=1S/C12H12NO3P/c14-17(15,16)9-12-7-6-11(8-13-12)10-4-2-1-3-5-10/h1-8H,9H2,(H2,14,15,16)
InChIKey 
JTYLHYFDHHMHKD-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
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
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 7

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

Ligand PDB entry

ChEMBL 41

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)