Ligand profile

Q9H

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

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

Via homolog PDB 6z61 UniProt Q8Y8D7 Formula C₂₅H₃₁N₁₁O₈
Mol. weight 613.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Q9H
PDB
6z61
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 613.59 Da
LogP (Crippen) -3.78
H-bond donors 8
H-bond acceptors 19
TPSA 280.11 Ų
Rotatable bonds 9
Aromatic rings 4 / 6
Heavy atoms 44
Fraction sp³ C 0.52
Formula C₂₅H₃₁N₁₁O₈

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 280.1
  • −1 ≤ LogP ≤ 5 -3.78
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 613.6
  • LogP ≤ 5 -3.78
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 280.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(c(n2)C#CCOCC3C(C(C(O3)n4cnc5c4ncnc5NCCN)O)O)C6C(C(C(O6)CO)O)O)N
InChI 
InChI=1S/C25H31N11O8/c26-3-4-28-21-15-22(31-9-30-21)35(10-33-15)24-18(40)17(39)12(44-24)7-42-5-1-2-13-34-14-20(27)29-8-32-23(14)36(13)25-19(41)16(38)11(6-37)43-25/h8-12,16-19,24-25,37-41H,3-7,26H2,(H2,27,29,32)(H,28,30,31)
InChIKey 
SCMIFBNZCXBOAA-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' 'PF20143

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)