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MolNFT v1 · #125502 · protein

Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor npd-001

5LAQ · Camp-specific 3',5'-cyclic phosphodiesterase 4B,CAMP…: “Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor npd-001”. X-ray diffraction, 3 ligands (6M5, ZN, MG), 1 pocket (best druggability 0.71). MolNFT…

PDB
5LAQ
Type
protein
Length
337 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Camp-specific 3',5'-cyclic phosphodiesterase 4B,CAMP- specific 3',5'-cyclic…
EC
3.1.4.53
UniProt
Q07343
Ligands
6M5, ZN, MG
Pockets
1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 1% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACamp-specific 3',5'-cyclic phosphodiesterase 4B,CAMP- specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53)protein33765% helix, 1% strandQ07343

Ligands and binding sites

  • 6M5 · (4~{A}~{S},8~{A}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl) phenoxy]butoxy]phenyl]-4~{A},5,8,8~{A}-tetrahydrophthalazin-1-one · ligand · chains A
  • ZN · Zinc ion · metal · chains A
  • MG · Magnesium ion · metal · chains A
  • ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14720.710.8142MG, ACT, 6M5

Compared structures

  • 5LAQ · Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor NPD-001 · the same entry in another collection · chain A against A, TM-score 1.00

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