Ligand profile

C2G

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

Bound to: VK055_4017 — bifunctional protein RfaE, domain I

Via homolog PDB 1n1d UniProt P27623 Formula C₁₂H₂₁N₃O₁₃P₂
Mol. weight 477.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C2G
PDB
1n1d
UniProt (similar protein)
P27623
Target protein
VK055_4017

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 477.26 Da
LogP (Crippen) -2.95
H-bond donors 7
H-bond acceptors 14
TPSA 253.35 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.67
Formula C₁₂H₂₁N₃O₁₃P₂

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 253.3
  • −1 ≤ LogP ≤ 5 -2.95
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 477.3
  • LogP ≤ 5 -2.95
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 253.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](CO)O)O)O
InChI 
InChI=1S/C12H21N3O13P2/c13-8-1-2-15(12(20)14-8)11-10(19)9(18)7(27-11)5-26-30(23,24)28-29(21,22)25-4-6(17)3-16/h1-2,6-7,9-11,16-19H,3-5H2,(H,21,22)(H,23,24)(H2,13,14,20)/t6-,7+,9+,10+,11+/m0/s1
InChIKey 
HHPOUCCVONEPRK-CNYIRLTGSA-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
PF01467

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_4017.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)