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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-3098
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
- 6FTA
- Type
- protein
- Length
- 1,300 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
- E6N, ZN, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 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 | 329 | 66% helix, 1% 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 | 323 | 68% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- E6N · (4~{A}~{S},8~{A}~{S})-4-[4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl]-2-[1-(3-nitroimidazo[1, 2-b]pyridazin-6-yl)piperidin-4-yl]-4~{A},5,6,7,8, 8~{A}-hexahydrophthalazin-1-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 · 29 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 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 | 416 | 0.81 | 0.89 | 68 | EDO |
| 2 | 682 | 0.79 | 0.84 | 56 | EDO |
| 3 | 247 | 0.77 | 0.90 | 42 | EDO |
| 4 | 530 | 0.71 | 0.80 | 51 | MG, E6N |
| 5 | 157 | 0.71 | 0.90 | 28 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 1008 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 960 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 683 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 663 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6FTA · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098 · 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 6FTA · PDBe 6FTA · UniProt Q08499
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