Research workbench
New 5-benzylidenethiazolidine-4-one inhibitors of bacterial murd ligase: design, synthesis, crystal structures, and biological evaluation
Analyse New 5-benzylidenethiazolidine-4-one inhibitors of bacterial murd ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y67
- Type
- protein
- Length
- 435 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoylalanine--D-glutamate ligase
- EC
- 6.3.2.9
- UniProt
- P14900
- Ligands
- N21, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 435 | 36% helix, 22% strand | P14900 |
Ligands and binding sites
- N21 · (2R)-2-[[4-[[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]sulfonylamino]pentanedioic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.71 | 0.78 | 60 | N21, SO4 |
| 2 | 226 | 0.52 | 0.77 | 26 | empty |
| 3 | 162 | 0.49 | 0.78 | 28 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, carboxylation).
Compared structures
- 2Y67 · New 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design… · the same entry in another collection · chain A against A, TM-score 1.00
- P14900 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoylalanine-- D-glutamate ligase… · a predicted model of the same protein · chain A against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14900
- Elsewhere: RCSB PDB 2Y67 · PDBe 2Y67 · UniProt P14900
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