Ligand profile

9C2

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

Bound to: VK055_0991 — mannose-6-phosphate isomerase, class I

Via homolog PDB 5nw7 UniProt P34948 Formula C₅H₁₃N₂O₈P
Mol. weight 260.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9C2
PDB
5nw7
UniProt (similar protein)
P34948
Target protein
VK055_0991

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 260.14 Da
LogP (Crippen) -3.83
H-bond donors 7
H-bond acceptors 7
TPSA 182.57 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.80
Formula C₅H₁₃N₂O₈P

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 182.6
  • −1 ≤ LogP ≤ 5 -3.83
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 260.1
  • LogP ≤ 5 -3.83
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 182.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H](C(=O)NN)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C5H13N2O8P/c6-7-5(11)4(10)3(9)2(8)1-15-16(12,13)14/h2-4,8-10H,1,6H2,(H,7,11)(H2,12,13,14)/t2-,3-,4+/m1/s1
InChIKey 
ZPAONOPLWIBTOD-JJYYJPOSSA-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
PF20511

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_0991.

PDB 1

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)