Ligand profile

3PH

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

Bound to: VK055_0600 — respiratory nitrate reductase, gamma subunit

Via homolog PDB 1q16 UniProt P11350 Formula C₃₉H₇₇O₈P
Mol. weight 705.01 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PH
PDB
1q16
UniProt (similar protein)
P11350
Target protein
VK055_0600

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 705.01 Da
LogP (Crippen) 12.07
H-bond donors 2
H-bond acceptors 6
TPSA 119.36 Ų
Rotatable bonds 38
Aromatic rings 0 / 0
Heavy atoms 48
Fraction sp³ C 0.95
Formula C₃₉H₇₇O₈P

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 119.4
  • −1 ≤ LogP ≤ 5 12.07
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 705.0
  • LogP ≤ 5 12.07
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 38
  • TPSA ≤ 140 Ų 119.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCCCCCCCCCCCC
InChI 
InChI=1S/C39H77O8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-38(40)45-35-37(36-46-48(42,43)44)47-39(41)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h37H,3-36H2,1-2H3,(H2,42,43,44)/t37-/m1/s1
InChIKey 
YFWHNAWEOZTIPI-DIPNUNPCSA-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
PF02665' 'PF13247' 'PF14710

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_0600.

PDB 6

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)