Ligand profile

2BB

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 3k6l UniProt P0A6K3 Formula C₁₆H₃₁N₃O₅
Mol. weight 345.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2BB
PDB
3k6l
UniProt (similar protein)
P0A6K3
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.44 Da
LogP (Crippen) 0.13
H-bond donors 4
H-bond acceptors 5
TPSA 118.97 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 24
Fraction sp³ C 0.81
Formula C₁₆H₃₁N₃O₅

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 119.0
  • −1 ≤ LogP ≤ 5 0.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.4
  • LogP ≤ 5 0.13
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 119.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H]([C@@H](C(=O)NO)O)C(=O)N[C@H](C(=O)N(C)C)C(C)(C)C
InChI 
InChI=1S/C16H31N3O5/c1-9(2)8-10(11(20)14(22)18-24)13(21)17-12(16(3,4)5)15(23)19(6)7/h9-12,20,24H,8H2,1-7H3,(H,17,21)(H,18,22)/t10-,11+,12-/m1/s1
InChIKey 
USHCFFHZEHRVBD-GRYCIOLGSA-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
PF01327

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_3786.

PDB 11

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)