MolNFT v1 · #180336 · protein
Crystal structure of the catalytic domain of human PDE3A bound to dnmdp
7KWE · Cgmp-inhibited 3',5'-cyclic phosphodiesterase a: “Crystal structure of the catalytic domain of human PDE3A bound to dnmdp”. X-ray diffraction, 3 ligands (X5M, MN, MG), 13 pockets (best druggability 0.76). MolNFT v1 #180336 on…
- PDB
- 7KWE
- Type
- protein
- Length
- 1,464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase a
- EC
- 3.1.4.17
- UniProt
- Q14432
- Ligands
- X5M, MN, MG
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 363 | 60% helix, 2% strand | Q14432 |
| D | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 371 | 59% helix, 2% strand | Q14432 |
| C | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 365 | 61% helix, 2% strand | Q14432 |
| B | Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (EC 3.1.4.17) | protein | 365 | 59% helix, 2% strand | Q14432 |
Ligands and binding sites
- X5M · (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one · ligand · 4 copies · chains A, D, C, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, D, C, B
- ACT · Acetate ion · additive · 4 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.76 | 0.78 | 114 | ACT |
| 2 | 900 | 0.75 | 0.79 | 109 | X5M, MG |
| 3 | 747 | 0.75 | 0.79 | 81 | X5M, MG |
| 4 | 587 | 0.73 | 0.81 | 61 | X5M, MG |
| 5 | 468 | 0.71 | 0.81 | 50 | X5M, MG |
Interfaces
3 interfaces between chains.
- C–B · 1154 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 955 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7KWE · Crystal structure of the catalytic domain of human PDE3A bound to DNMDP · the same entry in another collection · chain B against B, TM-score 1.00
- Q14432 · AlphaFold monomer V2.0 prediction for cgmp-inhibited 3',5'-cyclic phosphodiesterase a… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q14432
- Elsewhere: RCSB PDB 7KWE · PDBe 7KWE · UniProt Q14432
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