Ligand profile

09C

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

Bound to: VK055_0078 — pyruvate kinase

Via homolog PDB 3t07 UniProt Q6GG09 Formula C₂₀H₁₆Br₂N₄O
Mol. weight 488.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
09C
PDB
3t07
UniProt (similar protein)
Q6GG09
Target protein
VK055_0078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.18 Da
LogP (Crippen) 4.68
H-bond donors 4
H-bond acceptors 2
TPSA 72.71 Ų
Rotatable bonds 2
Aromatic rings 4 / 5
Heavy atoms 27
Fraction sp³ C 0.15
Formula C₂₀H₁₆Br₂N₄O

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 72.7
  • −1 ≤ LogP ≤ 5 4.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 488.2
  • LogP ≤ 5 4.68
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 72.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1Br)[nH]cc2[C@H]3C(=O)NCC(N3)c4c[nH]c5c4ccc(c5)Br
InChI 
InChI=1S/C20H16Br2N4O/c21-10-1-3-12-14(7-23-16(12)5-10)18-9-25-20(27)19(26-18)15-8-24-17-6-11(22)2-4-13(15)17/h1-8,18-19,23-24,26H,9H2,(H,25,27)/t18?,19-/m0/s1
InChIKey 
OXVVLWOQGFZGEO-GGYWPGCISA-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
PF02887

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_0078.

PDB 9

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

Ligand PDB entry

ChEMBL 54

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)