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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-635
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
- 7A9V
- Type
- protein
- Length
- 1,303 residues
- Chains
- 4
- 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
- R5Z, ZN, MG
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 4 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 | 67% 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 | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 66% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 325 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- R5Z · 1-cycloheptyl-3-[4-methoxy-3-(2-phenylethoxy)phenyl]-4, 4-dimethyl-4,5-dihydro-1H-pyrazol-5-one · ligand · 3 copies · chains 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 · 33 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.73 | 0.91 | 22 | empty |
| 2 | 409 | 0.72 | 0.83 | 36 | MG, EDO, R5Z |
| 3 | 437 | 0.72 | 0.82 | 45 | MG, EDO |
| 4 | 453 | 0.71 | 0.81 | 41 | MG, EDO, R5Z |
| 5 | 123 | 0.71 | 0.92 | 33 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 915 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 912 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 799 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7A9V · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-635 · 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 7A9V · PDBe 7A9V · UniProt Q08499
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