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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-769
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
- 7ABE
- Type
- protein
- Length
- 1,304 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
- J2E, ZN, MG
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 330 | 67% helix, 0% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 326 | 66% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- J2E · 1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4, 4-dimethyl-4,5-dihydro-1H-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 · 50 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, 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
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.86 | 0.89 | 106 | EDO |
| 2 | 155 | 0.74 | 0.92 | 21 | EDO |
| 3 | 428 | 0.73 | 0.83 | 39 | MG, EDO, J2E |
| 4 | 158 | 0.72 | 0.91 | 28 | EDO |
| 5 | 494 | 0.72 | 0.81 | 46 | MG, EDO, DMS, J2E |
Interfaces
6 interfaces between chains.
- A–C · 949 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 909 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 673 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 244 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7ABE · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-769 · the same entry in another collection · chain D against D, 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 7ABE · PDBe 7ABE · UniProt Q08499
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