Research workbench
Structure of compound 4 bound human phospholipase D2 catalytic domain
Analyse Structure of compound 4 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
- 6OHQ
- Type
- protein
- Length
- 1,157 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D2
- EC
- 3.1.4.4
- UniProt
- O14939
- Ligands
- MKA, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D2 (EC 3.1.4.4) | protein | 580 | 31% helix, 23% strand | O14939 |
| B | Phospholipase D2 (EC 3.1.4.4) | protein | 577 | 31% helix, 22% strand | O14939 |
Ligands and binding sites
- MKA · 4-fluoro-N-{(2S)-1-[4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propan-2-yl}benzamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.75 | 0.79 | 76 | SO4 |
| 2 | 450 | 0.75 | 0.83 | 41 | MKA, SO4 |
| 3 | 514 | 0.74 | 0.82 | 45 | MKA, SO4 |
| 4 | 379 | 0.61 | 0.77 | 30 | empty |
| 5 | 348 | 0.60 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 6OHQ · PDBe 6OHQ · UniProt O14939
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