Ligand profile

VBN

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

Bound to: VK055_1926 — periplasmic binding family protein

Via homolog PDB 3r5t UniProt Q9RCF6 Formula C₃₅H₃₉N₅O₁₁
Mol. weight 705.72 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
VBN
PDB
3r5t
UniProt (similar protein)
Q9RCF6
Target protein
VK055_1926

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 705.72 Da
LogP (Crippen) 1.84
H-bond donors 8
H-bond acceptors 13
TPSA 243.07 Ų
Rotatable bonds 13
Aromatic rings 3 / 5
Heavy atoms 51
Fraction sp³ C 0.34
Formula C₃₅H₃₉N₅O₁₁

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 243.1
  • −1 ≤ LogP ≤ 5 1.84
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 705.7
  • LogP ≤ 5 1.84
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 243.1
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@H](N=C(O1)c2cccc(c2O)O)C(=O)NCCCN(CCCNC(=O)c3cccc(c3O)O)C(=O)[C@@H]4[C@H](OC(=N4)c5cccc(c5O)O)C
InChI 
InChI=1S/C35H39N5O11/c1-18-26(38-33(50-18)21-9-4-12-24(42)29(21)45)32(48)37-15-7-17-40(16-6-14-36-31(47)20-8-3-11-23(41)28(20)44)35(49)27-19(2)51-34(39-27)22-10-5-13-25(43)30(22)46/h3-5,8-13,18-19,26-27,41-46H,6-7,14-17H2,1-2H3,(H,36,47)(H,37,48)/t18-,19-,26+,27+/m1/s1
InChIKey 
LLMKLMMXMOTPRU-QCOILQKOSA-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
PF01497

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_1926.

PDB 10

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)