Ligand profile

U5A

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

Bound to: KP13_05231 — HpxD

Via homolog PDB 6wnd UniProt C3RVP5 Formula C₁₀H₁₇N₇O₂
Mol. weight 267.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U5A
PDB
6wnd
UniProt (similar protein)
C3RVP5
Target protein
KP13_05231

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 267.29 Da
LogP (Crippen) -1.72
H-bond donors 6
H-bond acceptors 4
TPSA 139.35 Ų
Rotatable bonds 2
Aromatic rings 0 / 3
Heavy atoms 19
Fraction sp³ C 0.70
Formula C₁₀H₁₇N₇O₂

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 139.4
  • −1 ≤ LogP ≤ 5 -1.72
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 267.3
  • LogP ≤ 5 -1.72
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 139.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C\1/N[C@H]2[C@@H](N/C(=N/[H])/N3[C@]2(N1)CCC3)COC(=O)N
InChI 
InChI=1S/C10H17N7O2/c11-7-15-6-5(4-19-9(13)18)14-8(12)17-3-1-2-10(6,17)16-7/h5-6H,1-4H2,(H2,12,14)(H2,13,18)(H3,11,15,16)/t5-,6-,10+/m0/s1
InChIKey 
WSPXQONARWJOKG-JFWOZONXSA-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
PF19112

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_05231.

PDB 7

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)