Ligand profile

RPD

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1qf4 UniProt P0A7D4 Formula C₁₃H₂₂N₃O₁₃P
Mol. weight 459.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RPD
PDB
1qf4
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 459.30 Da
LogP (Crippen) -3.66
H-bond donors 8
H-bond acceptors 11
TPSA 246.86 Ų
Rotatable bonds 10
Aromatic rings 0 / 2
Heavy atoms 30
Fraction sp³ C 0.77
Formula C₁₃H₂₂N₃O₁₃P

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 246.9
  • −1 ≤ LogP ≤ 5 -3.66
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 459.3
  • LogP ≤ 5 -3.66
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 246.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C[C@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)NC1=O
InChI 
InChI=1S/C13H22N3O13P/c17-5-16(24)6(10(20)21)2-1-3-15-11(22)13(14-12(15)23)9(19)8(18)7(29-13)4-28-30(25,26)27/h6-9,17-19,24H,1-5H2,(H,14,23)(H,20,21)(H2,25,26,27)/t6-,7-,8-,9-,13+/m1/s1
InChIKey 
MAXSFYCTFIBEAR-OJMIUMIFSA-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
PF00709

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_2887.

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)