Ligand profile

SFM

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

Bound to: KP13_00717 — Peptidyl-prolyl cis-trans isomerase A

Via homolog PDB 1nmk UniProt P62937 Formula C₃₉H₅₆N₄O₁₀
Mol. weight 740.90 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SFM
PDB
1nmk
UniProt (similar protein)
P62937
Target protein
KP13_00717

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 740.90 Da
LogP (Crippen) 1.77
H-bond donors 7
H-bond acceptors 11
TPSA 214.83 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 53
Fraction sp³ C 0.56
Formula C₃₉H₅₆N₄O₁₀

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 214.8
  • −1 ≤ LogP ≤ 5 1.77
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 740.9
  • LogP ≤ 5 1.77
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 214.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1[C@H](/C=C/C=C/C[C@H](OC(=O)[C@@H]2CCCN(N2)C(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H]([C@@H]1O)CCC(=O)C)C(C)C)Cc3cccc(c3)O)/C(=C/CO)/C)O
InChI 
InChI=1S/C39H56N4O10/c1-23(2)34-37(50)40-31(22-27-11-9-12-28(46)21-27)38(51)43-19-10-13-30(42-43)39(52)53-33(24(3)18-20-44)15-8-6-7-14-32(47)26(5)35(48)29(36(49)41-34)17-16-25(4)45/h6-9,11-12,14,18,21,23,26,29-35,42,44,46-48H,10,13,15-17,19-20,22H2,1-5H3,(H,40,50)(H,41,49)/b8-6+,14-7+,24-18+/t26-,29+,30-,31-,32-,33-,34-,35+/m0/s1
InChIKey 
WZVMDDRRINUPRQ-APBCKSDASA-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
PF00160

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_00717.

PDB 39

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

Ligand PDB entry

ChEMBL 100

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)