Ligand profile

0KX

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

Bound to: KP13_03062 — putative metal-dependent phosphohydrolase

Via homolog PDB 6txc UniProt Q9Y3Z3 Formula C₉H₁₇N₄O₁₂P₃
Mol. weight 466.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
0KX
PDB
6txc
UniProt (similar protein)
Q9Y3Z3
Target protein
KP13_03062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 466.17 Da
LogP (Crippen) -1.61
H-bond donors 7
H-bond acceptors 11
TPSA 252.99 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 28
Fraction sp³ C 0.56
Formula C₉H₁₇N₄O₁₂P₃

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 253.0
  • −1 ≤ LogP ≤ 5 -1.61
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 466.2
  • LogP ≤ 5 -1.61
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 253.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
InChI 
InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKey 
STYMTWKSQLVXJN-SHYZEUOFSA-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
PF01966

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_03062.

PDB 22

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

Ligand PDB entry

ChEMBL 1

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)