MolNFT v1 · #159204 · protein
Structure of compound 5 bound human phospholipase D1 catalytic domain
6OHR · Phospholipase D1, chimeric constuct: “Structure of compound 5 bound human phospholipase D1 catalytic domain”. X-ray diffraction, 1 ligand (MKG), 20 pockets (best druggability 0.83). MolNFT v1 #159204 on GenesisL1: 3D structure…
- PDB
- 6OHR
- Type
- protein
- Length
- 3,367 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D1, chimeric constuct
- EC
- 3.1.4.4
- UniProt
- Q13393
- Ligands
- MKG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 576 | 32% helix, 22% strand | Q13393 |
| B | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 569 | 33% helix, 23% strand | Q13393 |
| C | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 572 | 32% helix, 22% strand | Q13393 |
| D | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 564 | 32% helix, 23% strand | Q13393 |
| E | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 560 | 33% helix, 22% strand | Q13393 |
| F | Phospholipase D1, chimeric constuct (EC 3.1.4.4) | protein | 526 | 31% helix, 19% strand | Q13393 |
Ligands and binding sites
- MKG · 4-fluoro-N-{(2S)-1-[(5R)-5-(3-fluorophenyl)-2-oxo-1-oxa-3,9-diazaspiro[5.5]undecan-9-yl]propan-2-yl}benzamide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.83 | 0.84 | 135 | MKG |
| 2 | 280 | 0.80 | 0.92 | 47 | empty |
| 3 | 342 | 0.79 | 0.89 | 64 | empty |
| 4 | 1007 | 0.78 | 0.80 | 94 | empty |
| 5 | 831 | 0.78 | 0.81 | 82 | empty |
Interfaces
6 interfaces between chains.
- B–C · 802 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 763 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 721 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 683 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 266 Ų buried · 2 hydrogen bonds · protein-protein
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 Q13393
- Elsewhere: RCSB PDB 6OHR · PDBe 6OHR · UniProt Q13393
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