MolNFT v1 · #151739 · protein
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1335
6HWO · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-1335”. X-ray diffraction, 3 ligands (FFZ, ZN, MG), 14 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6HWO
- Type
- protein
- Length
- 1,296 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
- FFZ, ZN, MG
- Pockets
- 14 · best druggability 0.84
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 | 327 | 68% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 321 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 68% 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
- FFZ · 3-[5-[(4ar,8as)-4-oxidanylidene-3-propan-2-yl-4A,5,8, 8A-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-N-(phenylmethyl)prop-2-ynamide · 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 · 51 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains B, 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 | 627 | 0.84 | 0.88 | 72 | EDO, PEG |
| 2 | 245 | 0.75 | 0.89 | 41 | PEG, EDO |
| 3 | 151 | 0.73 | 0.91 | 18 | EDO |
| 4 | 446 | 0.72 | 0.82 | 41 | FFZ, MG |
| 5 | 475 | 0.71 | 0.81 | 40 | FFZ, MG |
Interfaces
6 interfaces between chains.
- A–C · 996 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 931 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 651 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 634 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 230 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6HWO · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335 · 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 6HWO · PDBe 6HWO · UniProt Q08499
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