MolNFT v1 · #114101 · protein

Crystal structure of human PDE1B with inhibitor 3

5B25 · CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide…: “Crystal structure of human PDE1B with inhibitor 3”. X-ray diffraction, 4 ligands (4QJ, ZN, MG), 13 pockets (best druggability 0.83). MolNFT v1 #114101 on GenesisL1: 3D…

PDB: 5B25
Type: protein
Length: 1,331 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
EC: 3.1.4.17
UniProt: Q01064
Ligands: 4QJ, ZN, MG, SO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17)	protein	335	69% helix, 0% strand	Q01064
B, C, D	CALCIUM/CALMODULIN-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (EC 3.1.4.17)	protein	332	70% helix, 0% strand	Q01064

Ligands and binding sites

4QJ · (11R,15S)-4-{[4-(6-fluoropyridin-2-yl)phenyl]methyl}-8-methyl-5-(phenylamino)-1,3,4,8,10-pentaazatetracyclo[7.6.0.02,6.011,15]pentadeca-2,5,9-trien-7-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
SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D
GOL · Glycerol · additive · 8 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	789	0.83	0.86	81	MG, 4QJ, GOL
2	952	0.81	0.82	67	SO4, GOL
3	1074	0.80	0.82	83	SO4
4	436	0.72	0.82	40	MG, 4QJ, GOL
5	415	0.72	0.82	39	MG, 4QJ, GOL

Interfaces

4 interfaces between chains.

A–C · 739 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 723 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 466 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

Q01064 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q01064
Elsewhere: RCSB PDB 5B25 · PDBe 5B25 · UniProt Q01064

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