Ligand profile

OK8

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

Bound to: KP13_03826 — Phosphoribosylaminoimidazole-succinocarboxamide synthase

Via homolog PDB 6yb8 UniProt P22234 Formula C₁₃H₁₉N₄O₁₂P
Mol. weight 454.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
OK8
PDB
6yb8
UniProt (similar protein)
P22234
Target protein
KP13_03826

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 454.29 Da
LogP (Crippen) -3.15
H-bond donors 8
H-bond acceptors 11
TPSA 263.99 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₄O₁₂P

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 264.0
  • −1 ≤ LogP ≤ 5 -3.15
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 454.3
  • LogP ≤ 5 -3.15
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 264.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)C(=O)N[C@@H](CC(=O)O)C(=O)O
InChI 
InChI=1S/C13H19N4O12P/c14-10-7(11(22)16-4(13(23)24)1-6(18)19)15-3-17(10)12-9(21)8(20)5(29-12)2-28-30(25,26)27/h3-5,8-9,12,20-21H,1-2,14H2,(H,16,22)(H,18,19)(H,23,24)(H2,25,26,27)/t4-,5+,8+,9+,12+/m0/s1
InChIKey 
NAQGHJTUZRHGAC-ZZZDFHIKSA-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
PF01259

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_03826.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 24

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)