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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-053
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
- 6RCW
- Type
- protein
- Length
- 1,301 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
- JX2, ZN, MG
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 66% 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, D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- JX2 · 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide · 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 · 38 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.87 | 0.89 | 116 | EDO, DTT |
| 2 | 418 | 0.72 | 0.83 | 39 | MG, EDO, JX2 |
| 3 | 437 | 0.72 | 0.82 | 42 | MG, EDO, JX2 |
| 4 | 131 | 0.72 | 0.92 | 17 | EDO |
| 5 | 165 | 0.72 | 0.90 | 33 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 916 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 913 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 668 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 223 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6RCW · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053 · 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 6RCW · PDBe 6RCW · UniProt Q08499
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