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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-768
Analyse Crystal structure of human phosphodiesterase 4D2 catalytic domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ABD
- Type
- protein
- Length
- 1,302 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.41
- Source
- Homo sapiens
- Molecule
- cAMP-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- RLW, ZN, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.41 · 3 distinct chains · 67% 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 | 330 | 66% helix, 1% strand | Q08499 |
| B | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 67% helix, 1% strand | Q08499 |
| C, D | cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- RLW · 3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,4-dimethyl-1~{H}-pyrazol-5-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.81 | 0.90 | 61 | EDO |
| 2 | 396 | 0.80 | 0.89 | 61 | EDO |
| 3 | 456 | 0.73 | 0.82 | 40 | MG, RLW |
| 4 | 443 | 0.73 | 0.83 | 40 | MG, RLW |
| 5 | 178 | 0.73 | 0.90 | 34 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 928 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 907 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 730 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 688 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 236 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7ABD · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-768 · 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 7ABD · PDBe 7ABD · UniProt Q08499
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