Ligand profile

7D4

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

Bound to: KP13_00998 — hypothetical protein

Via homolog PDB 5tk7 UniProt O24769 Formula C₁₀H₁₆N₅O₁₂P₃
Mol. weight 491.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7D4
PDB
5tk7
UniProt (similar protein)
O24769
Target protein
KP13_00998

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 491.18 Da
LogP (Crippen) -0.74
H-bond donors 6
H-bond acceptors 13
TPSA 258.90 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 30
Fraction sp³ C 0.50
Formula C₁₀H₁₆N₅O₁₂P₃

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 258.9
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 491.2
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 258.9
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](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)CO)N
InChI 
InChI=1S/C10H16N5O12P3/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(25-10)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-6,10,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6-,10-/m1/s1
InChIKey 
QPXUYEBFFPGHRP-OXOINMOOSA-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_00998.

PDB 4

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)