Ligand profile

CA6

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

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

Via homolog PDB 4em3 UniProt Q2FIA5 Formula C₂₄H₄₂N₇O₁₈P₃S
Mol. weight 841.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CA6
PDB
4em3
UniProt (similar protein)
Q2FIA5
Target protein
VK055_0231

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 841.62 Da
LogP (Crippen) -1.77
H-bond donors 9
H-bond acceptors 19
TPSA 380.70 Ų
Rotatable bonds 21
Aromatic rings 2 / 3
Heavy atoms 53
Fraction sp³ C 0.71
Formula C₂₄H₄₂N₇O₁₈P₃S

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 -1.77
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 841.6
  • LogP ≤ 5 -1.77
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 21
  • 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)C)O
InChI 
InChI=1S/C24H42N7O18P3S/c1-24(2,19(34)22(35)27-8-6-15(32)26-7-4-5-9-53(3,43)44)11-46-52(41,42)49-51(39,40)45-10-14-18(48-50(36,37)38)17(33)23(47-14)31-13-30-16-20(25)28-12-29-21(16)31/h12-14,17-19,23,33-34H,4-11H2,1-3H3,(H,26,32)(H,27,35)(H,39,40)(H,41,42)(H2,25,28,29)(H2,36,37,38)/t14-,17-,18-,19+,23-/m1/s1
InChIKey 
RMJJETDNMMDBND-NDZSKPAWSA-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)