Research workbench
Second-generation sulfonamide inhibitors of murd: activity optimisation with conformationally rigid analogues of D-glutamic acid
Analyse Second-generation sulfonamide inhibitors of murd: activity optimisation with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XPC
- 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
- Q8X9Y9
- Ligands
- 051, SO4, CL
- Pockets
- 3 · best druggability 0.73
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 | Q8X9Y9 |
Ligands and binding sites
- 051 · (1R,3R,4S)-4-[({6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl}sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.73 | 0.78 | 82 | 051, DMS, SO4 |
| 2 | 211 | 0.52 | 0.77 | 23 | empty |
| 3 | 61 | 0.30 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, carboxylation).
Compared structures
- 2XPC · Second-generation sulfonamide inhibitors of MurD: Activity optimisation with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X9Y9 · 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 0.93
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 Q8X9Y9
- Elsewhere: RCSB PDB 2XPC · PDBe 2XPC · UniProt Q8X9Y9
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