Research workbench
Structure of compound 3 (ML299) bound human phospholipase D2 catalytic domain
Analyse Structure of compound 3 (ML299) bound human phospholipase D2 catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OHS
- Type
- protein
- Length
- 2,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D2
- EC
- 3.1.4.4
- UniProt
- O14939
- Ligands
- MJY
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phospholipase D2 (EC 3.1.4.4) | protein | 584 | 31% helix, 22% strand | O14939 |
Ligands and binding sites
- MJY · 4-bromo-N-{(2S)-1-[1-(3-fluorophenyl)-4-oxo-1,3,8-triazaspiro[4.5]decan-8-yl]propan-2-yl}benzamide · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.82 | 0.87 | 62 | MJY |
| 2 | 644 | 0.82 | 0.86 | 73 | MJY |
| 3 | 718 | 0.78 | 0.83 | 90 | empty |
| 4 | 783 | 0.75 | 0.79 | 64 | empty |
| 5 | 737 | 0.75 | 0.80 | 65 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1077 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 864 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 844 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 62 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OHS · Structure of compound 3 (ML299) bound human Phospholipase D2 catalytic domain · the same entry in another collection · chain A against A, TM-score 1.00
- O14939 · AlphaFold monomer V2.0 prediction for phospholipase D2 (O14939) · a predicted model of the same protein · chain A 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 O14939
- Elsewhere: RCSB PDB 6OHS · PDBe 6OHS · UniProt O14939
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