MolNFT v1 · #125534 · protein

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-001

5LBO · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor npd-001”. X-ray diffraction, 3 ligands (6M5, ZN, MG), 14 pockets (best druggability 0.86). MolNFT v1…

PDB: 5LBO
Type: protein
Length: 1,301 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: 6M5, ZN, MG
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 4 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	66% helix, 1% strand	Q08499
C	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	323	67% helix, 1% strand	Q08499
D	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53)	protein	324	67% helix, 1% strand	Q08499

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 · 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 · 28 copies · chains A, B, C, D
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, C, B, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D

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

Pockets

14 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	710	0.86	0.89	97	EDO, DTT
2	1039	0.79	0.81	94	EDO
3	179	0.73	0.90	35	empty
4	431	0.72	0.82	39	MG, EDO, 6M5
5	470	0.72	0.81	45	MG, EDO, 6M5

Interfaces

6 interfaces between chains.

A–C · 937 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 915 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 726 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 661 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 223 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5LBO · Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001 · 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 5LBO · PDBe 5LBO · UniProt Q08499

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