Ligand profile

Q9N

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

Bound to: KP13_02430 — putative inorganic polyphosphate/ATP-NAD kinase

Via homolog PDB 6z65 UniProt Q8Y8D7 Formula C₂₇H₃₄N₁₂O₈
Mol. weight 654.65 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Q9N
PDB
6z65
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 654.65 Da
LogP (Crippen) -3.71
H-bond donors 8
H-bond acceptors 19
TPSA 302.97 Ų
Rotatable bonds 10
Aromatic rings 4 / 6
Heavy atoms 47
Fraction sp³ C 0.52
Formula C₂₇H₃₄N₁₂O₈

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 303.0
  • −1 ≤ LogP ≤ 5 -3.71
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 654.6
  • LogP ≤ 5 -3.71
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 303.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COCC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CNC(=O)CCCN)O)O)N)O)O)N
InChI 
InChI=1S/C27H34N12O8/c28-5-1-4-15(40)31-7-12-18(41)21(44)27(46-12)39-14(37-17-23(30)33-10-35-25(17)39)3-2-6-45-8-13-19(42)20(43)26(47-13)38-11-36-16-22(29)32-9-34-24(16)38/h9-13,18-21,26-27,41-44H,1,4-8,28H2,(H,31,40)(H2,29,32,34)(H2,30,33,35)
InChIKey 
FSTDOBBDPHECFF-UHFFFAOYSA-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
PF01513

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_02430.

PDB 51

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

Ligand PDB entry

ChEMBL 3

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)