Ligand profile

6AM

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

Bound to: VK055_4780 — cytidine and deoxycytidylate deaminase zinc-binding region family protein

Via homolog PDB 5xkq UniProt A0QY90 Formula C₃H₅N₅O
Mol. weight 127.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6AM
PDB
5xkq
UniProt (similar protein)
A0QY90
Target protein
VK055_4780

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 127.11 Da
LogP (Crippen) -1.26
H-bond donors 3
H-bond acceptors 6
TPSA 110.94 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.00
Formula C₃H₅N₅O

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 110.9
  • −1 ≤ LogP ≤ 5 -1.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 127.1
  • LogP ≤ 5 -1.26
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 110.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1(nc(nc(n1)O)N)N
InChI 
InChI=1S/C3H5N5O/c4-1-6-2(5)8-3(9)7-1/h(H5,4,5,6,7,8,9)
InChIKey 
MASBWURJQFFLOO-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
PF00383

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_4780.

PDB 11

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)