Ligand profile

0O2

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

Bound to: VK055_4376 — putative oxidoreductase

Via homolog PDB 6gfm UniProt P0ADR8 Formula C₁₀H₁₈N₅O₂₀P₅
Mol. weight 683.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0O2
PDB
6gfm
UniProt (similar protein)
P0ADR8
Target protein
VK055_4376

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 683.14 Da
LogP (Crippen) -2.10
H-bond donors 10
H-bond acceptors 17
TPSA 392.16 Ų
Rotatable bonds 12
Aromatic rings 2 / 3
Heavy atoms 40
Fraction sp³ C 0.50
Formula C₁₀H₁₈N₅O₂₀P₅

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 392.2
  • −1 ≤ LogP ≤ 5 -2.10
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 683.1
  • LogP ≤ 5 -2.10
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 392.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
InChI 
InChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKey 
KCPMACXZAITQAX-UUOKFMHZSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF14793

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_4376.

PDB 1

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)