Ligand profile

NDA

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

Bound to: VK055_2572 — thrA

Via homolog PDB 1ebu UniProt P31116 Formula C₂₁H₂₉N₇O₁₃P₂
Mol. weight 649.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NDA
PDB
1ebu
UniProt (similar protein)
P31116
Target protein
VK055_2572

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 649.45 Da
LogP (Crippen) -3.29
H-bond donors 7
H-bond acceptors 18
TPSA 304.02 Ų
Rotatable bonds 11
Aromatic rings 3 / 5
Heavy atoms 43
Fraction sp³ C 0.52
Formula C₂₁H₂₉N₇O₁₃P₂

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 304.0
  • −1 ≤ LogP ≤ 5 -3.29
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 649.4
  • LogP ≤ 5 -3.29
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 304.0
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)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)CN
InChI 
InChI=1S/C21H29N7O13P2/c22-4-10-2-1-3-27(5-10)20-16(31)14(29)11(39-20)6-37-42(33,34)41-43(35,36)38-7-12-15(30)17(32)21(40-12)28-9-26-13-18(23)24-8-25-19(13)28/h1-3,5,8-9,11-12,14-17,20-21,29-32H,4,6-7,22H2,(H3-,23,24,25,33,34,35,36)/t11-,12-,14-,15-,16-,17-,20-,21-/m1/s1
InChIKey 
HMCRLFVYYFBZEZ-PLEFRAQWSA-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
PF00742' 'PF03447

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_2572.

PDB 4

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)