Research workbench
Structural and kinetic evaluation of phosphoramidate inhibitors on thermolysin
Analyse Structural and kinetic evaluation of phosphoramidate inhibitors on thermolysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMS
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermolysin
- EC
- 3.4.24.27
- UniProt
- P43133
- Ligands
- OZH, CA, ZN
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Thermolysin (EC 3.4.24.27) | protein | 316 | 42% helix, 18% strand | P43133 |
Ligands and binding sites
- OZH · (2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino) ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid · ligand · chains E
- CA · Calcium ion · metal · 4 copies · chains E
- ZN · Zinc ion · metal · chains E
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains E
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.51 | 0.81 | 22 | OZH, TRS |
Compared structures
- 6YMS · Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin · the same entry in another collection · chain E against E, TM-score 1.00
- P43133 · AlphaFold monomer V2.0 prediction for thermolysin (P43133) · a predicted model of the same protein · chain E against A, TM-score 1.00
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 P43133
- Elsewhere: RCSB PDB 6YMS · PDBe 6YMS · UniProt P43133
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