Ligand profile

UMM

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

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

Via homolog PDB 6x3y UniProt P62937 Formula C₂₈H₄₂N₄O₇
Mol. weight 546.67 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
UMM
PDB
6x3y
UniProt (similar protein)
P62937
Target protein
KP13_00717

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 546.67 Da
LogP (Crippen) 2.47
H-bond donors 3
H-bond acceptors 8
TPSA 135.30 Ų
Rotatable bonds 4
Aromatic rings 1 / 3
Heavy atoms 39
Fraction sp³ C 0.64
Formula C₂₈H₄₂N₄O₇

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 135.3
  • −1 ≤ LogP ≤ 5 2.47
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 546.7
  • LogP ≤ 5 2.47
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 135.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@@H](C(=O)N[C@H]1Cc2cccc(c2)OCCCCOC(=O)[C@@H]3CCCN(C1=O)N3)NC(=O)OC(C)(C)C
InChI 
InChI=1S/C28H42N4O7/c1-18(2)23(30-27(36)39-28(3,4)5)24(33)29-22-17-19-10-8-11-20(16-19)37-14-6-7-15-38-26(35)21-12-9-13-32(31-21)25(22)34/h8,10-11,16,18,21-23,31H,6-7,9,12-15,17H2,1-5H3,(H,29,33)(H,30,36)/t21-,22-,23-/m0/s1
InChIKey 
BZQRBTRFLXZFDJ-VABKMULXSA-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)