Ligand profile

8F5

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

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

Via homolog PDB 5n0g UniProt D5AV08 Formula C₄₇H₆₂N₄O₁₄
Mol. weight 907.03 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8F5
PDB
5n0g
UniProt (similar protein)
D5AV08
Target protein
KP13_02326

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 907.03 Da
LogP (Crippen) 6.48
H-bond donors 8
H-bond acceptors 11
TPSA 310.21 Ų
Rotatable bonds 20
Aromatic rings 0 / 5
Heavy atoms 65
Fraction sp³ C 0.62
Formula C₄₇H₆₂N₄O₁₄

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 6.48
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 907.0
  • LogP ≤ 5 6.48
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 20
  • 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)/CC=C)(C)CC(=O)O)CCC(=O)O)(C)C)CCC(=O)O
InChI 
InChI=1S/C47H62N4O14/c1-9-10-24-39-27(13-16-33(56)57)46(7,22-37(64)65)47(8,51-39)42-28(19-35(60)61)44(5,18-17-34(58)59)40(50-42)23(2)38-26(12-15-32(54)55)43(3,4)30(49-38)20-29-25(11-14-31(52)53)45(6,21-36(62)63)41(24)48-29/h9,20,23,25,27-28,42,51H,1,10-19,21-22H2,2-8H3,(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)(H,64,65)/b29-20-,39-24-/t23-,25-,27-,28+,42-,44-,45+,46+,47+/m1/s1
InChIKey 
VXYZYIAZOLQLTR-JBBZEPTESA-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)