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MolNFT v1 · #76350 · protein

Crystal structure of PDE9A(Q453E) in complex with ibmx

3QI4 · High affinity cgmp-specific 3',5'-cyclic phosphodiesterase…: “Crystal structure of PDE9A(Q453E) in complex with ibmx”. X-ray diffraction, 3 ligands (IBM, ZN, MG), 5 pockets (best druggability 0.74). MolNFT v1 #76350 on GenesisL1: 3D…

PDB
3QI4
Type
protein
Length
650 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
EC
3.1.4.35
UniProt
O76083
Ligands
IBM, ZN, MG
Pockets
5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BHigh affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35)protein32570% helix, 0% strandO76083

Ligands and binding sites

  • IBM · 3-isobutyl-1-methylxanthine · ligand · 2 copies · chains A, B
  • ZN · Zinc ion · metal · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13720.740.8543IBM, MG
21340.700.9028empty
33180.700.8341IBM, MG
41490.480.7820empty
5510.330.7816empty

Interfaces

1 interface between chains.

  • A–B · 1092 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

  • 3QI4 · Crystal structure of PDE9A(Q453E) in complex with IBMX · the same entry in another collection · chain B against B, TM-score 1.00
  • O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98

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