Ligand profile

1YA

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

Bound to: VK055_3785 — methionyl-tRNA formyltransferase

Via homolog PDB 5vyu UniProt F8WJP6 Formula C₂₀H₂₃N₇O₇
Mol. weight 473.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1YA
PDB
5vyu
UniProt (similar protein)
F8WJP6
Target protein
VK055_3785

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 473.45 Da
LogP (Crippen) -0.73
H-bond donors 7
H-bond acceptors 9
TPSA 219.84 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.30
Formula C₂₀H₂₃N₇O₇

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 219.8
  • −1 ≤ LogP ≤ 5 -0.73
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 473.4
  • LogP ≤ 5 -0.73
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 219.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N(C[C@@H]2CNC3=C(N2)C(=O)NC(=N3)N)C=O
InChI 
InChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)23-11(7-22-16)8-27(9-28)12-3-1-10(2-4-12)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,11,13,23H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,22,25,26,32)/t11-,13-/m0/s1
InChIKey 
AUFGTPPARQZWDO-AAEUAGOBSA-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
PF00551

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_3785.

PDB 10

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)