Ligand profile

JB2

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

Bound to: VK055_3785 — methionyl-tRNA formyltransferase

Via homolog PDB 5vyu UniProt F8WJP6 Formula C₁₆H₂₆N₆O₁₄P₂
Mol. weight 588.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JB2
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 588.36 Da
LogP (Crippen) -3.63
H-bond donors 9
H-bond acceptors 17
TPSA 317.28 Ų
Rotatable bonds 8
Aromatic rings 2 / 4
Heavy atoms 38
Fraction sp³ C 0.69
Formula C₁₆H₂₆N₆O₁₄P₂

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 317.3
  • −1 ≤ LogP ≤ 5 -3.63
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 588.4
  • LogP ≤ 5 -3.63
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 317.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)N
InChI 
InChI=1S/C16H26N6O14P2/c1-4-6(17)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)22-3-19-7-12(22)20-16(18)21-13(7)27/h3-6,8-11,14-15,23-26H,2,17H2,1H3,(H,28,29)(H,30,31)(H3,18,20,21,27)/t4-,5-,6-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKey 
PMFIPWCEUCAMAY-YVXBHLEUSA-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)