Ligand profile

6IA

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

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog PDB 3epl UniProt P07884 Formula C₁₅H₂₄N₅O₇P
Mol. weight 417.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6IA
PDB
3epl
UniProt (similar protein)
P07884
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 417.36 Da
LogP (Crippen) 0.01
H-bond donors 5
H-bond acceptors 10
TPSA 172.08 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 28
Fraction sp³ C 0.67
Formula C₁₅H₂₄N₅O₇P

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 172.1
  • −1 ≤ LogP ≤ 5 0.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 417.4
  • LogP ≤ 5 0.01
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 172.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)CCNc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
InChI 
InChI=1S/C15H24N5O7P/c1-8(2)3-4-16-13-10-14(18-6-17-13)20(7-19-10)15-12(22)11(21)9(27-15)5-26-28(23,24)25/h6-9,11-12,15,21-22H,3-5H2,1-2H3,(H,16,17,18)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1
InChIKey 
GZJXCRHEMLAMRA-SDBHATRESA-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
PF01715

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_2895.

PDB 4

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)