Ligand profile

P8X

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

Bound to: KP13_02326 — Cobalt-precorrin-8X methylmutase

Via homolog PDB 4au1 UniProt D5AV08 Formula C₄₄H₅₈N₄O₁₄
Mol. weight 866.96 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P8X
PDB
4au1
UniProt (similar protein)
D5AV08
Target protein
KP13_02326

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 866.96 Da
LogP (Crippen) 5.53
H-bond donors 8
H-bond acceptors 11
TPSA 310.21 Ų
Rotatable bonds 18
Aromatic rings 0 / 5
Heavy atoms 62
Fraction sp³ C 0.64
Formula C₄₄H₅₈N₄O₁₄

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 310.2
  • −1 ≤ LogP ≤ 5 5.53
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 867.0
  • LogP ≤ 5 5.53
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 18
  • TPSA ≤ 140 Ų 310.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C2=C(C(C(=N2)/C=C\3/[C@H]([C@](C(=N3)/C=C\4/[C@H]([C@]([C@@](N4)([C@H]5[C@@H]([C@@](C1=N5)(C)CCC(=O)O)CC(=O)O)C)(C)CC(=O)O)CCC(=O)O)(C)CC(=O)O)CCC(=O)O)(C)C)CCC(=O)O
InChI 
InChI=1S/C44H58N4O14/c1-21-37-24(10-13-32(53)54)40(2,3)28(46-37)17-26-22(8-11-30(49)50)42(5,19-35(59)60)29(45-26)18-27-23(9-12-31(51)52)43(6,20-36(61)62)44(7,48-27)39-25(16-34(57)58)41(4,38(21)47-39)15-14-33(55)56/h17-18,21-23,25,39,48H,8-16,19-20H2,1-7H3,(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H,61,62)/b26-17-,27-18-/t21-,22-,23-,25+,39-,41-,42+,43+,44+/m1/s1
InChIKey 
LIJKCTVSMYEQAC-IBWMGOEXSA-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
PF02570

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_02326.

PDB 4

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)