Ligand profile

BC9

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

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog PDB 4ttv UniProt P26639 Formula C₂₇H₄₃NO₆
Mol. weight 477.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BC9
PDB
4ttv
UniProt (similar protein)
P26639
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 477.64 Da
LogP (Crippen) 4.47
H-bond donors 3
H-bond acceptors 6
TPSA 127.85 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 34
Fraction sp³ C 0.81
Formula C₂₇H₄₃NO₆

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 127.9
  • −1 ≤ LogP ≤ 5 4.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 477.6
  • LogP ≤ 5 4.47
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 127.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1CC(CC(C(C(=CCCCC(OC(=O)CC(C(C1)C)O)C2CCC2C(=O)O)C#N)O)C)C
InChI 
InChI=1S/C27H43NO6/c1-16-11-17(2)13-19(4)26(31)20(15-28)7-5-6-8-24(21-9-10-22(21)27(32)33)34-25(30)14-23(29)18(3)12-16/h7,16-19,21-24,26,29,31H,5-6,8-14H2,1-4H3,(H,32,33)
InChIKey 
KHMHNBNVTBTHJD-UHFFFAOYSA-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
PF00587

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_0276.

PDB 11

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

Ligand PDB entry

ChEMBL 28

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)