Research workbench
Crystal structure of the PDE4D catalytic domain in complex with gebr- 32A
Analyse Crystal structure of the PDE4D catalytic domain in complex with gebr- 32A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FDC
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- DD5, D5N, MG, ZN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 329 | 65% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- DD5 · (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol · ligand · chains A
- D5N · (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.72 | 0.82 | 45 | MG, D5N |
| 2 | 449 | 0.70 | 0.80 | 46 | MG, DD5 |
| 3 | 195 | 0.58 | 0.81 | 19 | empty |
| 4 | 224 | 0.57 | 0.79 | 29 | EDO |
| 5 | 69 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 771 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6FDC · Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a · the same entry in another collection · 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 Q08499
- Elsewhere: RCSB PDB 6FDC · PDBe 6FDC · UniProt Q08499
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