3HDZ: PDB entry 3HDZ

Identification, Synthesis, and SAR of Amino Substituted Pyrido[3,2b]pryaziones as Potent and Selective PDE5 Inhibitors. Determined by X-ray diffraction at 1.8 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,026
Mol. weight: 37.74 kDa
Ligands: PD6, ZN, MG
Released: 7 Jul 2009

Explore 3HDZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3HDZ contains 24 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	539-545	7
α-helix	547-550	4
α-helix	551-554	4
α-helix	568-581	14
α-helix	592-604	13
α-helix	615-630	16
α-helix	635-637	3
α-helix	640-652	13
α-helix	662-667	6
α-helix	671-675	5
α-helix	681-694	15
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-797	26
α-helix	800-802	3
α-helix	803-805	3
α-helix	807-812	6
α-helix	813-820	8
α-helix	821-825	5
α-helix	826-835	10
α-helix	837-839	3
α-helix	840-857	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cGMP-specific 3',5'-cyclic phosphodiesterase,cAMP-specific 3',5'-cyclic phosphodiesterase…	A	protein	324	Homo sapiens	O76074 (AlphaFold model), P27815 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3HDZ_1 cGMP-specific 3',5'-cyclic phosphodiesterase,cAMP-specific 3',5'-cyclic phosphodiesterase 4A,cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
ETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVL
CRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDL
DHPGVSNQFLINTNSELALMYNDESVLEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLK
IIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHEKELFLAMLMTACDLSAITKPWPI
QQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTH
VSEDCFPLLDGCRKNRQKWQALAE

Ligands and cofactors

ID	Name	Formula	Copies
PD6	5-amino-1-butyl-7-phenyl-1,6-naphthyridin-4(1H)-one	C18 H19 N3 O	1
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1

Primary citation

Identification, synthesis and SAR of amino substituted pyrido[3,2b]pyrazinones as potent and selective PDE5 inhibitors. Owen, D.R., Walker, J.K., Jon Jacobsen, E. et al. Bioorg Med Chem Lett (2009) 19:4088-4091. DOI 10.1016/j.bmcl.2009.06.012 · PubMed

Other PDB entries of the same protein (UniProt O76074 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TBF 1.3 Å, Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil
1XOZ 1.37 Å, Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil
5JO3 1.49 Å, PDE5A for NaV1.7
2CHM 1.6 Å, Crystal structure of N2 substituted pyrazolo pyrimidinones - a flipped binding mode in…
1XP0 1.79 Å, Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil
3HC8 1.79 Å, Investigation of Aminopyridiopyrazinones as PDE5 Inhibitors: Evaluation of Modifications…
2H44 1.8 Å, Crystal structure of PDE5A1 in complex with icarisid II
8W4S 1.85 Å, Crystal structure of PDE5A in complex with CVT-313
2H40 1.85 Å, Crystal structure of the catalytic domain of unliganded PDE5
3TGG 1.91 Å, A novel series of potent and selective PDE5 inhibitor2
6L6E 1.92 Å, Human PDE5 catalytic core in complex with avanafil
3SIE 1.93 Å, Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

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