Ligand profile

6X4

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

Bound to: VK055_4617 — membrane-bound lytic murein transglycosylase F

Via homolog PDB 5aa4 UniProt A0A1I9GEN8 Formula C₂₀H₃₇N₆O₈⁺
Mol. weight 489.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6X4
PDB
5aa4
UniProt (similar protein)
A0A1I9GEN8
Target protein
VK055_4617

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 489.55 Da
LogP (Crippen) -3.89
H-bond donors 8
H-bond acceptors 7
TPSA 244.66 Ų
Rotatable bonds 16
Aromatic rings 0 / 0
Heavy atoms 34
Fraction sp³ C 0.70
Formula C₂₀H₃₇N₆O₈⁺

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 244.7
  • −1 ≤ LogP ≤ 5 -3.89
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 489.6
  • LogP ≤ 5 -3.89
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 244.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](C(=O)N)NC(=O)C(CCCC[NH3+])NC(=O)CC[C@H](C(=O)O)NC(=O)[C@H](C)NC(=O)[C@@H](C)O
InChI 
InChI=1S/C20H36N6O8/c1-10(16(22)29)23-19(32)13(6-4-5-9-21)25-15(28)8-7-14(20(33)34)26-17(30)11(2)24-18(31)12(3)27/h10-14,27H,4-9,21H2,1-3H3,(H2,22,29)(H,23,32)(H,24,31)(H,25,28)(H,26,30)(H,33,34)/p+1/t10-,11+,12-,13?,14-/m1/s1
InChIKey 
NEROIIRQSNQGCX-LNXOKTMHSA-O

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
PF00497

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_4617.

ZINC 50

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

Compound Similarity (Tanimoto)