Ligand profile

NPW

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

Bound to: VK055_2899 — putative carbohydrate kinase

Via homolog PDB 3rpz UniProt P94368 Formula C₂₁H₃₂N₇O₁₈P₃
Mol. weight 763.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NPW
PDB
3rpz
UniProt (similar protein)
P94368
Target protein
VK055_2899

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 763.44 Da
LogP (Crippen) -3.37
H-bond donors 10
H-bond acceptors 20
TPSA 384.38 Ų
Rotatable bonds 13
Aromatic rings 2 / 5
Heavy atoms 49
Fraction sp³ C 0.62
Formula C₂₁H₃₂N₇O₁₈P₃

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 384.4
  • −1 ≤ LogP ≤ 5 -3.37
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 763.4
  • LogP ≤ 5 -3.37
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 20
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 384.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=C(CC[C@@H]5O)C(=O)N)O)O)O)OP(=O)(O)O)N
InChI 
InChI=1S/C21H32N7O18P3/c22-17-12-19(25-6-24-17)28(7-26-12)21-16(45-47(34,35)36)14(31)10(44-21)5-42-49(39,40)46-48(37,38)41-4-9-13(30)15(32)20(43-9)27-3-8(18(23)33)1-2-11(27)29/h3,6-7,9-11,13-16,20-21,29-32H,1-2,4-5H2,(H2,23,33)(H,37,38)(H,39,40)(H2,22,24,25)(H2,34,35,36)/t9-,10-,11+,13-,14-,15-,16-,20-,21-/m1/s1
InChIKey 
SZKXTJUOKARGIY-VPHRTNKSSA-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
PF01256

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_2899.

PDB 9

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)