MolNFT v1 · #172638 · protein
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-654
7A8Q · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-654”. X-ray diffraction, 3 ligands (R4H, ZN, MG), 12 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 7A8Q
- Type
- protein
- Length
- 1,302 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
- R4H, ZN, MG
- Pockets
- 12 · 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 | 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 | 67% 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
- R4H · 2-cycloheptyl-5-[4-methoxy-3-[[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]methoxy]phenyl]-4,4-dimethyl-pyrazolidin-3-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 · 27 copies · chains A, C, D, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.84 | 0.89 | 107 | EDO |
| 2 | 749 | 0.78 | 0.82 | 55 | EDO |
| 3 | 266 | 0.77 | 0.90 | 51 | EDO |
| 4 | 470 | 0.72 | 0.82 | 44 | MG, EDO, R4H |
| 5 | 445 | 0.72 | 0.82 | 40 | MG, EDO, R4H, PEG |
Interfaces
6 interfaces between chains.
- B–D · 926 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 785 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 706 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7A8Q · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-654 · 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 7A8Q · PDBe 7A8Q · UniProt Q08499
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