Ligand profile

0X1

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

Bound to: VK055_0552 — fused predicted DNA-binding transcriptional regulator and predicted amino transferase

Via homolog PDB 4gdy UniProt Q8N5Z0 Formula C₂₄H₂₂N₅O₇P
Mol. weight 523.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0X1
PDB
4gdy
UniProt (similar protein)
Q8N5Z0
Target protein
VK055_0552

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 523.44 Da
LogP (Crippen) 3.60
H-bond donors 5
H-bond acceptors 9
TPSA 171.30 Ų
Rotatable bonds 8
Aromatic rings 5 / 5
Heavy atoms 37
Fraction sp³ C 0.12
Formula C₂₄H₂₂N₅O₇P

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 171.3
  • −1 ≤ LogP ≤ 5 3.60
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 523.4
  • LogP ≤ 5 3.60
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 171.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3cc(ccc3N4C2=NNC4=O)Oc5ccccc5)O
InChI 
InChI=1S/C24H22N5O7P/c1-14-22(30)19(16(11-25-14)13-35-37(32,33)34)12-26-20-10-15-9-18(36-17-5-3-2-4-6-17)7-8-21(15)29-23(20)27-28-24(29)31/h2-11,26,30H,12-13H2,1H3,(H,28,31)(H2,32,33,34)
InChIKey 
AMDYNPYMOMDDSQ-UHFFFAOYSA-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
PF00155

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_0552.

PDB 19

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

Ligand PDB entry

ChEMBL 100

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)