Ligand profile

5FA

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

Bound to: KP13_04863 — Phosphatase nudJ

Via homolog PDB 1vc8 UniProt Q75UV1 Formula C₁₀H₁₈N₅O₁₉P₅
Mol. weight 667.14 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5FA
PDB
1vc8
UniProt (similar protein)
Q75UV1
Target protein
KP13_04863

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 667.14 Da
LogP (Crippen) -1.40
H-bond donors 9
H-bond acceptors 18
TPSA 372.19 Ų
Rotatable bonds 12
Aromatic rings 2 / 3
Heavy atoms 39
Fraction sp³ C 0.50
Formula C₁₀H₁₈N₅O₁₉P₅

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 372.2
  • −1 ≤ LogP ≤ 5 -1.40
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 667.1
  • LogP ≤ 5 -1.40
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 372.2
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)O[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O)N
InChI 
InChI=1S/C10H18N5O19P5/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(30-10)1-29-36(21,22)32-38(25,26)34-39(27,28)33-37(23,24)31-35(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey 
WYJWVZZCMBUPSP-KQYNXXCUSA-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
PF00293

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_04863.

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)