MolNFT v1 · #152233 · protein
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-417
6IBF · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-417”. X-ray diffraction, 3 ligands (4I7, ZN, MG), 15 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6IBF
- 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
- 4I7, ZN, MG
- Pockets
- 15 · best druggability 0.80
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 | 66% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 323 | 67% 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
- 4I7 · (4~{A}~{S},8~{A}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3, 2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{A},5,8,8~{A}-tetrahydrophthalazin-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 · 38 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 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
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 | 398 | 0.80 | 0.89 | 64 | EDO |
| 2 | 627 | 0.79 | 0.85 | 52 | EDO |
| 3 | 272 | 0.78 | 0.90 | 45 | EDO |
| 4 | 156 | 0.71 | 0.90 | 32 | EDO |
| 5 | 489 | 0.71 | 0.81 | 49 | MG, 4I7 |
Interfaces
6 interfaces between chains.
- A–C · 1029 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 931 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 674 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6IBF · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417 · 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 6IBF · PDBe 6IBF · UniProt Q08499
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