Ligand profile

59C

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

Bound to: VK055_2094 — htpG

Via homolog PDB 4asa UniProt P02829 Formula C₃₂H₄₅N₃O₈
Mol. weight 599.73 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
59C
PDB
4asa
UniProt (similar protein)
P02829
Target protein
VK055_2094

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 599.73 Da
LogP (Crippen) 2.93
H-bond donors 4
H-bond acceptors 9
TPSA 166.28 Ų
Rotatable bonds 6
Aromatic rings 0 / 2
Heavy atoms 43
Fraction sp³ C 0.50
Formula C₃₂H₄₅N₃O₈

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 166.3
  • −1 ≤ LogP ≤ 5 2.93
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 599.7
  • LogP ≤ 5 2.93
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 166.3
PAINS Alert

Matches PAINS filter: quinone_A(370). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1C[C@@H]([C@@H]([C@@H](C=C([C@H]([C@H](/C=C/C=C(C(=O)NC2=C(C(=O)C(=C(C1)C2=O)NCC=C)C)C)OC)OC(=O)N)C)C)O)OC
InChI 
InChI=1S/C32H45N3O8/c1-9-13-34-26-22-14-17(2)15-24(42-8)27(36)19(4)16-20(5)30(43-32(33)40)23(41-7)12-10-11-18(3)31(39)35-25(29(22)38)21(6)28(26)37/h9-12,16-17,19,23-24,27,30,34,36H,1,13-15H2,2-8H3,(H2,33,40)(H,35,39)/b12-10+,18-11?,20-16?/t17-,19-,23+,24+,27-,30-/m1/s1
InChIKey 
BMVOZLNYIKNSKD-PKBVXAQJSA-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
PF02518

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_2094.

PDB 27

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

Ligand PDB entry

ChEMBL 6

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)