Ligand profile

PUM

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

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

Via homolog PDB 5x21 UniProt Q8RQE8 Formula C₁₇H₂₆N₈O₉
Mol. weight 486.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PUM
PDB
5x21
UniProt (similar protein)
Q8RQE8
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 486.44 Da
LogP (Crippen) -5.32
H-bond donors 10
H-bond acceptors 10
TPSA 290.04 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 34
Fraction sp³ C 0.53
Formula C₁₇H₂₆N₈O₉

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 290.0
  • −1 ≤ LogP ≤ 5 -5.32
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 486.4
  • LogP ≤ 5 -5.32
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 290.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCC(=O)N([C@@H](CCC(=O)N)C(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)C2=CNC(=O)NC2=O)O)O)O
InChI 
InChI=1S/C17H26N8O9/c18-9(26)2-1-7(25(33)10(27)5-22-16(19)20)15(31)21-4-8-11(28)12(29)13(34-8)6-3-23-17(32)24-14(6)30/h3,7-8,11-13,28-29,33H,1-2,4-5H2,(H2,18,26)(H,21,31)(H4,19,20,22)(H2,23,24,30,32)/t7-,8+,11+,12+,13-/m0/s1
InChIKey 
XDEYHXABZOKKDZ-YFKLLHAASA-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' 'PF04565' 'PF04998

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)