Ligand profile

XJS

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

Bound to: KP13_00629 — DNA polymerase I

Via homolog PDB 3ojs UniProt P19821 Formula C₃₈H₆₃N₈O₂₀P₃
Mol. weight 1044.88 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XJS
PDB
3ojs
UniProt (similar protein)
P19821
Target protein
KP13_00629

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 1044.88 Da
LogP (Crippen) -1.09
H-bond donors 9
H-bond acceptors 17
TPSA 392.37 Ų
Rotatable bonds 30
Aromatic rings 1 / 2
Heavy atoms 69
Fraction sp³ C 0.68
Formula C₃₈H₆₃N₈O₂₀P₃

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 392.4
  • −1 ≤ LogP ≤ 5 -1.09
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 1044.9
  • LogP ≤ 5 -1.09
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 17
Veber's rules Fail
  • Rotatable bonds ≤ 10 30
  • TPSA ≤ 140 Ų 392.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCN(CC)C(=O)CCC(=O)NCCCN(CCCNC(=O)CCC(=O)N(CC)CC)C(=O)CCC(=O)NCC#CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
InChI 
InChI=1S/C38H63N8O20P3/c1-5-43(6-2)33(51)16-13-31(49)40-20-10-22-45(23-11-21-41-32(50)14-17-34(52)44(7-3)8-4)35(53)18-15-30(48)39-19-9-12-27-25-46(38(55)42-37(27)54)36-24-28(47)29(64-36)26-63-68(59,60)66-69(61,62)65-67(56,57)58/h25,28-29,36,47H,5-8,10-11,13-24,26H2,1-4H3,(H,39,48)(H,40,49)(H,41,50)(H,59,60)(H,61,62)(H,42,54,55)(H2,56,57,58)
InChIKey 
FRKZJUQJYOJKOB-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
PF00476

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_00629.

PDB 34

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)