Ligand profile

GGM

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

Bound to: VK055_2907 — ribosome small subunit-dependent GTPase A

Via homolog PDB 5uz4 UniProt P39286 Formula C₁₈H₂₄N₇O₁₄P₃
Mol. weight 655.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GGM
PDB
5uz4
UniProt (similar protein)
P39286
Target protein
VK055_2907

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 655.35 Da
LogP (Crippen) -0.86
H-bond donors 9
H-bond acceptors 15
TPSA 320.00 Ų
Rotatable bonds 11
Aromatic rings 3 / 4
Heavy atoms 42
Fraction sp³ C 0.33
Formula C₁₈H₂₄N₇O₁₄P₃

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 320.0
  • −1 ≤ LogP ≤ 5 -0.86
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 655.3
  • LogP ≤ 5 -0.86
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 320.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNc1ccccc1C(=O)O[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3N=C(NC4=O)N)CO[P@](=O)(O)O[P@](=O)(NP(=O)(O)O)O
InChI 
InChI=1S/C18H24N7O14P3/c1-20-9-5-3-2-4-8(9)17(28)38-13-10(6-36-42(34,35)39-41(32,33)24-40(29,30)31)37-16(12(13)26)25-7-21-11-14(25)22-18(19)23-15(11)27/h2-5,7,10,12-13,16,20,26H,6H2,1H3,(H,34,35)(H3,19,22,23,27)(H4,24,29,30,31,32,33)/t10-,12-,13-,16-/m1/s1
InChIKey 
ZGTKZICAFACDSP-XNIJJKJLSA-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
PF03193

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_2907.

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)