MolNFT v1 · #117613 · protein
Human PDE10A in complex with 3-(2-chloro-5-phenyl-3H-imidazol-4-yl)-1- (3-trifluoromethoxy-phenyl)-1H-pyridazin-4-one at 2.30A
5EDG · Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase…: “Human PDE10A in complex with 3-(2-chloro-5-phenyl-3H-imidazol-4-yl)-1…”. X-ray diffraction, 3 ligands (5MG, ZN, MG), 20 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 5EDG
- Type
- protein
- Length
- 1,254 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17, 3.1.4.35
- UniProt
- Q9Y233
- Ligands
- 5MG, ZN, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 313 | 72% helix, 0% strand | Q9Y233 |
| B | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 315 | 70% helix, 0% strand | Q9Y233 |
| D | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 313 | 68% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 5MG · 3-(2-chloranyl-5-phenyl-1~{H}-imidazol-4-yl)-1-[3-(trifluoromethyloxy)phenyl]pyridazin-4-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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.74 | 0.83 | 44 | MG, 5MG |
| 2 | 441 | 0.73 | 0.83 | 50 | MG, 5MG |
| 3 | 420 | 0.73 | 0.83 | 43 | MG, 5MG |
| 4 | 412 | 0.73 | 0.83 | 47 | MG, 5MG |
| 5 | 615 | 0.73 | 0.80 | 66 | empty |
Interfaces
5 interfaces between chains.
- B–C · 731 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 714 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 706 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 540 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (artifact, disulfide).
Compared structures
- 5EDG · CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH… · the same entry in another collection · chain B against B, 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 Q9Y233
- Elsewhere: RCSB PDB 5EDG · PDBe 5EDG · UniProt Q9Y233
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