Ligand profile

ATR

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

Bound to: VK055_4724 — putative alcohol dehydrogenase in ethanolamine utilization

Via homolog PDB 6c75 UniProt A0A0Q2QQL1 Formula C₁₀H₁₆N₅O₁₃P₃
Mol. weight 507.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ATR
PDB
6c75
UniProt (similar protein)
A0A0Q2QQL1
Target protein
VK055_4724

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 507.18 Da
LogP (Crippen) -1.63
H-bond donors 7
H-bond acceptors 13
TPSA 279.13 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 31
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₅O₁₃P₃

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 279.1
  • −1 ≤ LogP ≤ 5 -1.63
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 507.2
  • LogP ≤ 5 -1.63
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 279.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(27-29(17,18)19)6(16)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKey 
YPTPYQSAVGGMFN-KQYNXXCUSA-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
PF00465

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_4724.

PDB 3

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)