Ligand profile

5CY

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

Bound to: HT085_RS00010 — DNA polymerase III subunit beta

Via homolog PDB 3bep UniProt P0A988 Formula C₃₁H₃₉N₂O₂⁺
Mol. weight 471.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5CY
PDB
3bep
UniProt (similar protein)
P0A988
Target protein
HT085_RS00010

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 471.67 Da
LogP (Crippen) 5.62
H-bond donors 2
H-bond acceptors 3
TPSA 46.71 Ų
Rotatable bonds 9
Aromatic rings 2 / 4
Heavy atoms 35
Fraction sp³ C 0.39
Formula C₃₁H₃₉N₂O₂⁺

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 46.7
  • −1 ≤ LogP ≤ 5 5.62
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 471.7
  • LogP ≤ 5 5.62
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 46.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(c2ccccc2[N+](=C1/C=C/C=C/C=C/3\C(c4ccccc4N3CCCO)(C)C)CCCO)C
InChI 
InChI=1S/C31H39N2O2/c1-30(2)24-14-8-10-16-26(24)32(20-12-22-34)28(30)18-6-5-7-19-29-31(3,4)25-15-9-11-17-27(25)33(29)21-13-23-35/h5-11,14-19,34-35H,12-13,20-23H2,1-4H3/q+1
InChIKey 
VFBDPICHYNKCQJ-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
PF00712' 'PF02767

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00010.

PDB 18

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

Ligand PDB entry

ChEMBL 5

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)