Ligand profile

K3H

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

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

Via homolog PDB 6rgc UniProt Q8Y8D7 Formula C₂₄H₂₉N₁₁O₇
Mol. weight 583.57 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K3H
PDB
6rgc
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 583.57 Da
LogP (Crippen) -3.66
H-bond donors 7
H-bond acceptors 18
TPSA 262.09 Ų
Rotatable bonds 6
Aromatic rings 4 / 6
Heavy atoms 42
Fraction sp³ C 0.50
Formula C₂₄H₂₉N₁₁O₇

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 262.1
  • −1 ≤ LogP ≤ 5 -3.66
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 583.6
  • LogP ≤ 5 -3.66
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 18
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 262.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(CC#Cc1nc2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)CC4C(C(C(O4)n5cnc6c5ncnc6N)O)O
InChI 
InChI=1S/C24H29N11O7/c1-33(5-10-15(37)17(39)23(41-10)34-9-31-13-19(25)27-7-29-21(13)34)4-2-3-12-32-14-20(26)28-8-30-22(14)35(12)24-18(40)16(38)11(6-36)42-24/h7-11,15-18,23-24,36-40H,4-6H2,1H3,(H2,25,27,29)(H2,26,28,30)
InChIKey 
OPWBYPZWGGCZGG-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)