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Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-656

Analyse Crystal structure of human phosphodiesterase 4D2 catalytic domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AB9
Type: protein
Length: 1,302 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-specific 3',5'-cyclic phosphodiesterase 4D
EC: 3.1.4.53
UniProt: Q08499
Ligands: QWZ, ZN, MG
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	330	66% helix, 1% strand	Q08499
B	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499
C, D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499

Ligands and binding sites

QWZ · 1-cycloheptyl-3-{4-methoxy-3-[2-(4-methoxyphenyl) ethoxy]phenyl}-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-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
EDO · 1,2-ethanediol · additive · 31 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains C, D

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	468	0.82	0.89	70	EDO
2	1047	0.78	0.80	96	EDO
3	248	0.76	0.89	48	EDO
4	449	0.71	0.81	40	MG, EDO, QWZ
5	468	0.71	0.81	44	MG, EDO, QWZ

Interfaces

6 interfaces between chains.

A–C · 920 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 910 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 799 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 684 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 240 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7AB9 · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-656 · the same entry in another collection · chain A against A, 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 Q08499
Elsewhere: RCSB PDB 7AB9 · PDBe 7AB9 · UniProt Q08499

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