Ligand profile

K2H

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

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

Via homolog PDB 6rg7 UniProt Q8Y8D7 Formula C₁₉H₂₁N₁₁O₃
Mol. weight 451.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K2H
PDB
6rg7
UniProt (similar protein)
Q8Y8D7
Target protein
KP13_02430

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 451.45 Da
LogP (Crippen) -1.74
H-bond donors 5
H-bond acceptors 13
TPSA 203.03 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 33
Fraction sp³ C 0.37
Formula C₁₉H₂₁N₁₁O₃

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 203.0
  • −1 ≤ LogP ≤ 5 -1.74
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 451.5
  • LogP ≤ 5 -1.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 203.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(CC#Cc1[nH]c2c(n1)c(ncn2)N)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
InChI 
InChI=1S/C19H21N11O3/c1-29(4-2-3-10-27-11-15(20)22-6-24-17(11)28-10)5-9-13(31)14(32)19(33-9)30-8-26-12-16(21)23-7-25-18(12)30/h6-9,13-14,19,31-32H,4-5H2,1H3,(H2,21,23,25)(H3,20,22,24,27,28)
InChIKey 
MNFDLXSVTTXDGC-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)