Ligand profile

DND

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

Bound to: VK055_1987 — oxygen-insensitive NAD(P)H nitroreductase

Via homolog PDB 5j8d UniProt Q01234 Formula C₂₁H₂₇N₆O₁₅P₂⁺
Mol. weight 665.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DND
PDB
5j8d
UniProt (similar protein)
Q01234
Target protein
VK055_1987

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 665.42 Da
LogP (Crippen) -2.42
H-bond donors 8
H-bond acceptors 17
TPSA 312.47 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 44
Fraction sp³ C 0.48
Formula C₂₁H₂₇N₆O₁₅P₂⁺

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 312.5
  • −1 ≤ LogP ≤ 5 -2.42
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 665.4
  • LogP ≤ 5 -2.42
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 312.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
InChI 
InChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,19-,20-/m1/s1
InChIKey 
SENPVEZBRZQVST-HISDBWNOSA-O

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
PF00881

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_1987.

PDB 14

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)