Ligand profile

BB1

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

Bound to: VK055_3786 — peptide deformylase

Via homolog PDB 1g27 UniProt P0A6K3 Formula C₁₆H₃₁N₃O₄
Mol. weight 329.44 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BB1
PDB
1g27
UniProt (similar protein)
P0A6K3
Target protein
VK055_3786

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 329.44 Da
LogP (Crippen) 1.26
H-bond donors 2
H-bond acceptors 4
TPSA 89.95 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 0.81
Formula C₁₆H₃₁N₃O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 90.0
  • −1 ≤ LogP ≤ 5 1.26
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 329.4
  • LogP ≤ 5 1.26
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 90.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC[C@H](CN(C=O)O)C(=O)N[C@H](C(=O)N(C)C)C(C)(C)C
InChI 
InChI=1S/C16H31N3O4/c1-7-8-9-12(10-19(23)11-20)14(21)17-13(16(2,3)4)15(22)18(5)6/h11-13,23H,7-10H2,1-6H3,(H,17,21)/t12-,13-/m1/s1
InChIKey 
AVDLWYHBABSSHC-CHWSQXEVSA-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)