Ligand profile

YQP

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

Bound to: KP13_02726 — S-adenosylmethionine synthase

Via homolog PDB 7lnh UniProt P31153 Formula C₁₄H₂₁N₃O₇S
Mol. weight 375.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YQP
PDB
7lnh
UniProt (similar protein)
P31153
Target protein
KP13_02726

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 375.40 Da
LogP (Crippen) -2.34
H-bond donors 5
H-bond acceptors 8
TPSA 167.87 Ų
Rotatable bonds 7
Aromatic rings 1 / 2
Heavy atoms 25
Fraction sp³ C 0.57
Formula C₁₄H₂₁N₃O₇S

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 167.9
  • −1 ≤ LogP ≤ 5 -2.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 375.4
  • LogP ≤ 5 -2.34
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 167.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=S(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O
InChI 
InChI=1S/C14H21N3O7S/c1-25(5-3-7(15)13(21)22)6-8-10(19)11(20)12(24-8)17-4-2-9(18)16-14(17)23/h2,4,7-8,10-12,19-20H,1,3,5-6,15H2,(H,21,22)(H,16,18,23)/t7-,8+,10+,11+,12+,25?/m0/s1
InChIKey 
HBPDMWXHIXRRKQ-OJANYLEWSA-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
PF00438' 'PF02772' 'PF02773

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_02726.

PDB 19

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)