Ligand profile

2U4

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

Bound to: KP13_00697 — Penicillin-binding protein 1A

Via homolog PDB 4oon UniProt Q07806 Formula C₂₅H₂₄N₆O₁₄S
Mol. weight 664.56 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
2U4
PDB
4oon
UniProt (similar protein)
Q07806
Target protein
KP13_00697

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 664.56 Da
LogP (Crippen) -1.00
H-bond donors 7
H-bond acceptors 16
TPSA 318.00 Ų
Rotatable bonds 15
Aromatic rings 2 / 3
Heavy atoms 46
Fraction sp³ C 0.28
Formula C₂₅H₂₄N₆O₁₄S

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 318.0
  • −1 ≤ LogP ≤ 5 -1.00
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 664.6
  • LogP ≤ 5 -1.00
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 318.0
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CO/N=C(\C[C@@H](C(=O)O)N2C(=O)c3cc(c(cc3C2=O)O)O)/C(=O)O)C=O
InChI 
InChI=1S/C25H24N6O14S/c1-25(2,23(42)43)45-30-17(13-8-46-24(26)28-13)18(35)27-9(6-32)7-44-29-12(21(38)39)5-14(22(40)41)31-19(36)10-3-15(33)16(34)4-11(10)20(31)37/h3-4,6,8-9,14,33-34H,5,7H2,1-2H3,(H2,26,28)(H,27,35)(H,38,39)(H,40,41)(H,42,43)/b29-12+,30-17-/t9-,14+/m1/s1
InChIKey 
VQOKWLNYKDCOTA-RCFVXGSMSA-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
PF00905

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_00697.

PDB 10

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

Ligand PDB entry

ChEMBL 7

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)