1XP0: Catalytic Domain Of Human Phosphodiesterase 5A

Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil. Determined by X-ray diffraction at 1.79 Å resolution. Released 14 Dec 2004.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,829
Mol. weight: 42.41 kDa
Ligands: VDN, MG, ZN
Released: 14 Dec 2004

Explore 1XP0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XP0 contains 25 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: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	535-545	11
α-helix	551-554	4
α-helix	568-581	14
α-helix	584-587	4
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	680-693	14
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-792	21
α-helix	793-797	5
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	840-856	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cGMP-specific 3',5'-cyclic phosphodiesterase	A	protein	364	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1XP0_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
MGSSHHHHHHSSGLVPRGSHMEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETA
LCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAG
KIQNKLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYNDESVLEHHHFDQCLM
ILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQ
KELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKN
KIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQ
AKRN

Ligands and cofactors

ID	Name	Formula	Copies
VDN	2-{2-ethoxy-5-[(4-ethylpiperazin-1-yl)sulfonyl]phenyl}-5-methyl-7-propylimidazo…	C23 H32 N6 O4 S	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Primary citation

Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. Card, G.L., England, B.P., Suzuki, Y. et al. Structure (2004) 12:2233-2247. DOI 10.1016/j.str.2004.10.004 · 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…
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
3HDZ 1.8 Å, Identification, Synthesis, and SAR of Amino Substituted Pyrido[3,2b]pryaziones as Potent…
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

Browse structure collections

About this viewer

MolViewer shows 1XP0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.