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MolNFT v1 · #138028 · protein

PDE1B complexed with compound 3S

5W6E · CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide…: “PDE1B complexed with compound 3S”. X-ray diffraction, 3 ligands (0NY, ZN, MG), 4 pockets (best druggability 0.71). MolNFT v1 #138028 on GenesisL1: 3D structure, binding sites…

PDB
5W6E
Type
protein
Length
321 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
EC
3.1.4.17
UniProt
Q01064
Ligands
0NY, ZN, MG
Pockets
4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17)protein32172% helix, 0% strandQ01064

Ligands and binding sites

  • 0NY · 7,8-dimethoxy-N-[(2S)-1-(3-methyl-1H-pyrazol-5-yl) propan-2-yl]quinazolin-4-amine · ligand · chains A
  • ZN · Zinc ion · metal · chains A
  • MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13650.710.8337MG, 0NY
2510.420.8312empty
3620.310.7516empty
4500.280.7513empty

Compared structures

  • 5W6E · PDE1b complexed with compound 3S · the same entry in another collection · chain A against A, TM-score 1.00
  • Q01064 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.99

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