MolNFT v1 · #111828 · protein
The structure of human PDE12 residues 161-609 in complex with GSK3036342A
4Z2B · 2',5'-phosphodiesterase 12: “The structure of human PDE12 residues 161-609 in complex with GSK3036342A”. X-ray diffraction, 3 ligands (4LC, MG, SO4), 4 pockets (best druggability 0.61). MolNFT v1 #111828 on GenesisL1: 3D structure…
- PDB
- 4Z2B
- Type
- protein
- Length
- 449 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2',5'-phosphodiesterase 12
- EC
- 3.1.4.-, 3.1.13.4
- UniProt
- Q6L8Q7
- Ligands
- 4LC, MG, SO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2',5'-phosphodiesterase 12 (EC 3.1.4.-, 3.1.13.4) | protein | 449 | 27% helix, 29% strand | Q6L8Q7 |
Ligands and binding sites
- 4LC · 3-(6-{[(2S,3S)-3-(hydroxymethyl)-2-phenylmorpholin-4-yl]carbonyl}-1-methyl-1H-benzimidazol-2-yl)-1H-indole-6-carbonitrile · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.61 | 0.77 | 41 | SO4, EDO, 4LC, MG |
| 2 | 118 | 0.55 | 0.83 | 20 | empty |
| 3 | 117 | 0.44 | 0.77 | 19 | empty |
| 4 | 59 | 0.29 | 0.74 | 13 | empty |
Compared structures
- 4Z2B · The structure of human PDE12 residues 161-609 in complex with GSK3036342A · the same entry in another collection · chain A against A, TM-score 1.00
- Q6L8Q7 · AlphaFold monomer V2.0 prediction for 2',5'-phosphodiesterase 12 (Q6L8Q7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q6L8Q7
- Elsewhere: RCSB PDB 4Z2B · PDBe 4Z2B · UniProt Q6L8Q7
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