Ligand profile

3CM

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

Bound to: VK055_3615 — nickel-responsive transcriptional regulator NikR

Via homolog PDB 2hza UniProt P0A6Z6 Formula C₂₁H₃₈O₁₁
Mol. weight 466.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3CM
PDB
2hza
UniProt (similar protein)
P0A6Z6
Target protein
VK055_3615

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 466.52 Da
LogP (Crippen) -2.01
H-bond donors 7
H-bond acceptors 11
TPSA 178.53 Ų
Rotatable bonds 9
Aromatic rings 0 / 3
Heavy atoms 32
Fraction sp³ C 1.00
Formula C₂₁H₃₈O₁₁

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 178.5
  • −1 ≤ LogP ≤ 5 -2.01
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 466.5
  • LogP ≤ 5 -2.01
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 178.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)CCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
InChI 
InChI=1S/C21H38O11/c22-9-12-14(24)15(25)17(27)21(30-12)32-19-13(10-23)31-20(18(28)16(19)26)29-8-4-7-11-5-2-1-3-6-11/h11-28H,1-10H2/t12-,13-,14-,15+,16-,17-,18-,19-,20-,21-/m1/s1
InChIKey 
FDBLAHXBTQUZSM-ZESVGKPKSA-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
PF01402' 'PF08753

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_3615.

ZINC 50

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

Compound Similarity (Tanimoto)