Ligand profile

6FY

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

Bound to: VK055_0721 — putative gamma-glutamyltransferase ywrD

Via homolog PDB 5b5t UniProt P18956 Formula C₁₀H₁₉N₂O₇P
Mol. weight 310.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6FY
PDB
5b5t
UniProt (similar protein)
P18956
Target protein
VK055_0721

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 310.24 Da
LogP (Crippen) -0.74
H-bond donors 4
H-bond acceptors 6
TPSA 156.02 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.70
Formula C₁₀H₁₉N₂O₇P

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 156.0
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 310.2
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 156.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@H](C(=O)NCC(=O)O)O[P@H](=O)CC[C@@H](C(=O)O)N
InChI 
InChI=1S/C10H19N2O7P/c1-2-7(9(15)12-5-8(13)14)19-20(18)4-3-6(11)10(16)17/h6-7,20H,2-5,11H2,1H3,(H,12,15)(H,13,14)(H,16,17)/t6-,7+/m0/s1
InChIKey 
ZHBIUULHWXYKFH-NKWVEPMBSA-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
PF01019

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_0721.

PDB 7

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)