Ligand profile

CA8

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

Bound to: VK055_0231 — nitrite reductase [NAD(P)H], small subunit

Via homolog PDB 4em4 UniProt Q2FIA5 Formula C₂₉H₄₄N₇O₁₈P₃S
Mol. weight 903.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CA8
PDB
4em4
UniProt (similar protein)
Q2FIA5
Target protein
VK055_0231

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 903.69 Da
LogP (Crippen) -0.34
H-bond donors 9
H-bond acceptors 19
TPSA 380.70 Ų
Rotatable bonds 22
Aromatic rings 3 / 4
Heavy atoms 58
Fraction sp³ C 0.55
Formula C₂₉H₄₄N₇O₁₈P₃S

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 380.7
  • −1 ≤ LogP ≤ 5 -0.34
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 903.7
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 22
  • TPSA ≤ 140 Ų 380.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCCCS(=O)(=O)c4ccccc4)O
InChI 
InChI=1S/C29H44N7O18P3S/c1-29(2,24(39)27(40)32-12-10-20(37)31-11-6-7-13-58(48,49)18-8-4-3-5-9-18)15-51-57(46,47)54-56(44,45)50-14-19-23(53-55(41,42)43)22(38)28(52-19)36-17-35-21-25(30)33-16-34-26(21)36/h3-5,8-9,16-17,19,22-24,28,38-39H,6-7,10-15H2,1-2H3,(H,31,37)(H,32,40)(H,44,45)(H,46,47)(H2,30,33,34)(H2,41,42,43)/t19-,22-,23-,24+,28-/m1/s1
InChIKey 
VRGBEUJWLKBAGR-VXAHOBLNSA-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
PF02852' 'PF07992

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_0231.

PDB 6

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

Ligand PDB entry

ZINC 26

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

Compound Similarity (Tanimoto)