Ligand profile

2KH

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

Bound to: KP13_01361 — DNA-directed RNA polymerase subunit beta'

Via homolog PDB 5w51 UniProt P04050 Formula C₉H₁₆N₃O₁₄P₃
Mol. weight 483.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2KH
PDB
5w51
UniProt (similar protein)
P04050
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 483.16 Da
LogP (Crippen) -2.93
H-bond donors 8
H-bond acceptors 11
TPSA 267.17 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 29
Fraction sp³ C 0.56
Formula C₉H₁₆N₃O₁₄P₃

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 267.2
  • −1 ≤ LogP ≤ 5 -2.93
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 483.2
  • LogP ≤ 5 -2.93
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 267.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
InChI 
InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
InChIKey 
OZIBFYOFLVBDIY-XVFCMESISA-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
PF00562' 'PF00623' 'PF05000

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_01361.

PDB 34

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

Ligand PDB entry

ChEMBL 2

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)