Ligand profile

1MG

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 5afi UniProt P0CE48 Formula C₁₁H₁₆N₅O₈P
Mol. weight 377.25 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1MG
PDB
5afi
UniProt (similar protein)
P0CE48
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 377.25 Da
LogP (Crippen) -2.56
H-bond donors 5
H-bond acceptors 11
TPSA 195.18 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.55
Formula C₁₁H₁₆N₅O₈P

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 195.2
  • −1 ≤ LogP ≤ 5 -2.56
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 377.3
  • LogP ≤ 5 -2.56
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 195.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1C(=O)c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C1N
InChI 
InChI=1S/C11H16N5O8P/c1-15-9(19)5-8(14-11(15)12)16(3-13-5)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H2,12,14)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKey 
RQNAZTAAOUHEIL-KQYNXXCUSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00237' 'PF00297

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_3750.

PDB 19

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)