Ligand profile

9WY

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

Bound to: KP13_04492 — hypothetical protein

Via homolog PDB 5w4z UniProt A0A3B6UEK8 Formula C₁₇H₂₁N₄O₉P
Mol. weight 456.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9WY
PDB
5w4z
UniProt (similar protein)
A0A3B6UEK8
Target protein
KP13_04492

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 456.35 Da
LogP (Crippen) -1.61
H-bond donors 6
H-bond acceptors 10
TPSA 208.09 Ų
Rotatable bonds 7
Aromatic rings 1 / 3
Heavy atoms 31
Fraction sp³ C 0.41
Formula C₁₇H₂₁N₄O₉P

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 208.1
  • −1 ≤ LogP ≤ 5 -1.61
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 456.3
  • LogP ≤ 5 -1.61
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 208.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC([C@@H]([C@@H](CO)O)OP(=O)(O)O)O
InChI 
InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(23)14(12(24)6-22)30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11?,12-,14+/m1/s1
InChIKey 
XTUPYSORVVXTTQ-AOUZGSJDSA-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
PF00296

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_04492.

PDB 6

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)