MolNFT v1 · #172688 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-617

7AAG · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-617”. X-ray diffraction, 3 ligands (QWT, MG, ZN), 15 pockets (best druggability 0.83). MolNFT v1…

PDB: 7AAG
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: QWT, MG, ZN
Pockets: 15 · best druggability 0.83

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

QWT · 1-cycloheptyl-3-(4-methoxy-3-{4-[4-(1H-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy}phenyl)-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 5 copies · chains A, C, B, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 50 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 12 copies · chains A, B, D, C
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	466	0.83	0.90	70	EDO, PEG
2	501	0.83	0.89	72	EDO, PEG
3	326	0.81	0.91	42	DMS, EDO
4	421	0.72	0.82	39	MG, QWT, EDO
5	423	0.72	0.82	45	MG, QWT, EDO

Interfaces

6 interfaces between chains.

B–D · 972 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 962 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 668 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 656 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 216 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7AAG · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-617 · 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 7AAG · PDBe 7AAG · UniProt Q08499

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.