Ligand profile

STD

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

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

Via homolog PDB 1zyr UniProt Q8RQE8 Formula C₃₂H₄₄N₂O₉
Mol. weight 600.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
STD
PDB
1zyr
UniProt (similar protein)
Q8RQE8
Target protein
KP13_01361

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 600.71 Da
LogP (Crippen) 2.46
H-bond donors 3
H-bond acceptors 9
TPSA 147.16 Ų
Rotatable bonds 7
Aromatic rings 0 / 5
Heavy atoms 43
Fraction sp³ C 0.66
Formula C₃₂H₄₄N₂O₉

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 147.2
  • −1 ≤ LogP ≤ 5 2.46
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 600.7
  • LogP ≤ 5 2.46
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 147.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@H]2C=C[C@@]3(CO3)[C@](O2)(O[C@@H]1[C@H](C)\C=C(/C)\C=C\C(=C/4\C(=O)[C@@H](N(C4=O)[C@@H]5CC[C@@H]([C@@H](O5)C)O)[C@H](C)C(=O)NC)\O)C
InChI 
InChI=1S/C32H44N2O9/c1-16(14-17(2)28-18(3)23-12-13-32(15-40-32)31(6,42-23)43-28)8-9-22(36)25-27(37)26(19(4)29(38)33-7)34(30(25)39)24-11-10-21(35)20(5)41-24/h8-9,12-14,17-21,23-24,26,28,35-36H,10-11,15H2,1-7H3,(H,33,38)/b9-8+,16-14+,25-22+/t17-,18+,19+,20+,21+,23-,24+,26+,28-,31-,32-/m1/s1
InChIKey 
KVTPRMVXYZKLIG-NCAOFHFGSA-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
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)