Ligand profile

GEK

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

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog PDB 4gek UniProt C3T5M2 Formula C₁₆H₂₂N₆O₇S
Mol. weight 442.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GEK
PDB
4gek
UniProt (similar protein)
C3T5M2
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 442.45 Da
LogP (Crippen) -5.85
H-bond donors 4
H-bond acceptors 12
TPSA 227.21 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.56
Formula C₁₆H₂₂N₆O₇S

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 227.2
  • −1 ≤ LogP ≤ 5 -5.85
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 442.5
  • LogP ≤ 5 -5.85
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 227.2
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)C[S@+](CC[C@@H](C(=O)[O-])[NH3+])CC(=O)[O-])O)O)N
InChI 
InChI=1S/C16H22N6O7S/c17-7(16(27)28)1-2-30(4-9(23)24)3-8-11(25)12(26)15(29-8)22-6-21-10-13(18)19-5-20-14(10)22/h5-8,11-12,15,25-26H,1-4,17H2,(H3-,18,19,20,23,24,27,28)/t7-,8+,11+,12+,15+,30-/m0/s1
InChIKey 
VFFTYSZNZJBRBG-HEOPWLPUSA-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
PF13649

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01630.

PDB 2

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)