Ligand profile

SYC

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

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

Via homolog PDB 3anl UniProt P45568 Formula C₆H₈NO₃P
Mol. weight 173.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SYC
PDB
3anl
UniProt (similar protein)
P45568
Target protein
VK055_2379

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 173.11 Da
LogP (Crippen) 0.76
H-bond donors 2
H-bond acceptors 2
TPSA 70.42 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.17
Formula C₆H₈NO₃P

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 0.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 173.1
  • LogP ≤ 5 0.76
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 70.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)CP(=O)(O)O
InChI 
InChI=1S/C6H8NO3P/c8-11(9,10)5-6-3-1-2-4-7-6/h1-4H,5H2,(H2,8,9,10)
InChIKey 
WVWCWWLEFNGDBC-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
PF08436

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)