Ligand profile

RC1

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

Bound to: VK055_1548 — 3-phosphoshikimate 1-carboxyvinyltransferase

Via homolog PDB 1x8t UniProt P0A6D3 Formula C₁₀H₁₆O₁₃P₂
Mol. weight 406.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RC1
PDB
1x8t
UniProt (similar protein)
P0A6D3
Target protein
VK055_1548

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 406.17 Da
LogP (Crippen) -1.40
H-bond donors 7
H-bond acceptors 7
TPSA 228.35 Ų
Rotatable bonds 7
Aromatic rings 0 / 1
Heavy atoms 25
Fraction sp³ C 0.60
Formula C₁₀H₁₆O₁₃P₂

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 228.3
  • −1 ≤ LogP ≤ 5 -1.40
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 406.2
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 228.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@](C(=O)O)(O[C@@H]1CC(=C[C@H]([C@H]1O)OP(=O)(O)O)C(=O)O)P(=O)(O)O
InChI 
InChI=1S/C10H16O13P2/c1-10(9(14)15,24(16,17)18)22-5-2-4(8(12)13)3-6(7(5)11)23-25(19,20)21/h3,5-7,11H,2H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)(H2,19,20,21)/t5-,6-,7+,10-/m1/s1
InChIKey 
HUOJJMMXOWLGJU-QGOVLLJGSA-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
PF00275

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_1548.

PDB 9

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

Ligand PDB entry

ChEMBL 14

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)