MolNFT v1 · #148675 · protein
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-226
6FDI · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-226”. X-ray diffraction, 3 ligands (D5T, ZN, MG), 16 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6FDI
- 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
- D5T, ZN, MG
- Pockets
- 16 · best druggability 0.85
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 | 330 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 68% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 326 | 67% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 68% helix, 1% strand | Q08499 |
Ligands and binding sites
- D5T · 1-[2-[4-[(4~{A}~{S},8~{A}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{A},5,8,8~{A}-tetrahydrophthalazin-2-yl]piperidin-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione · 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 · 59 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C
- PG4 · Tetraethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.85 | 0.90 | 84 | EDO |
| 2 | 242 | 0.77 | 0.90 | 42 | PEG, EDO |
| 3 | 161 | 0.74 | 0.92 | 21 | EDO |
| 4 | 407 | 0.72 | 0.83 | 40 | MG, EDO, D5T |
| 5 | 456 | 0.71 | 0.81 | 46 | MG, EDO, D5T |
Interfaces
6 interfaces between chains.
- B–D · 918 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 690 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 668 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 248 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6FDI · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226 · the same entry in another collection · chain C against C, 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 6FDI · PDBe 6FDI · UniProt Q08499
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