Ligand profile

C0K

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

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

Via homolog PDB 3r0i UniProt P45568 Formula C₁₁H₁₄F₂NO₅P
Mol. weight 309.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C0K
PDB
3r0i
UniProt (similar protein)
P45568
Target protein
VK055_2379

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 309.20 Da
LogP (Crippen) 1.81
H-bond donors 3
H-bond acceptors 3
TPSA 98.07 Ų
Rotatable bonds 5
Aromatic rings 1 / 1
Heavy atoms 20
Fraction sp³ C 0.36
Formula C₁₁H₁₄F₂NO₅P

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 98.1
  • −1 ≤ LogP ≤ 5 1.81
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 309.2
  • LogP ≤ 5 1.81
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 98.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C(=O)CC[C@@H](c1ccc(c(c1)F)F)P(=O)(O)O)O
InChI 
InChI=1S/C11H14F2NO5P/c1-14(16)11(15)5-4-10(20(17,18)19)7-2-3-8(12)9(13)6-7/h2-3,6,10,16H,4-5H2,1H3,(H2,17,18,19)/t10-/m0/s1
InChIKey 
IZWIBRNXHRUNKD-JTQLQIEISA-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' '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)