Ligand profile

UHB

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

Bound to: VK055_3566 — ankyrin repeat family protein

Via homolog PDB 4bj9 UniProt Q9H2K2 Formula C₂₄H₂₇N₉O₆
Mol. weight 537.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UHB
PDB
4bj9
UniProt (similar protein)
Q9H2K2
Target protein
VK055_3566

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 537.54 Da
LogP (Crippen) -1.95
H-bond donors 5
H-bond acceptors 12
TPSA 201.06 Ų
Rotatable bonds 5
Aromatic rings 3 / 6
Heavy atoms 39
Fraction sp³ C 0.42
Formula C₂₄H₂₇N₉O₆

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 201.1
  • −1 ≤ LogP ≤ 5 -1.95
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 537.5
  • LogP ≤ 5 -1.95
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 201.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(c(c1)NC(=O)CN3CCN(CC3)C(=O)[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)CNC2=O
InChI 
InChI=1S/C24H27N9O6/c25-20-16-21(28-10-27-20)33(11-29-16)24-18(36)17(35)19(39-24)23(38)32-6-4-31(5-7-32)9-15(34)30-14-3-1-2-12-13(14)8-26-22(12)37/h1-3,10-11,17-19,24,35-36H,4-9H2,(H,26,37)(H,30,34)(H2,25,27,28)/t17-,18+,19-,24+/m0/s1
InChIKey 
DDFLFKTXUWPNMV-UAKAABGRSA-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
PF00644

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_3566.

PDB 124

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)