3B2R: PDE5A1 catalytic domain

Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil. Determined by X-ray diffraction at 2.07 Å resolution. Released 20 May 2008.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,967
Mol. weight: 77.38 kDa
Ligands: VDN
Released: 20 May 2008

Explore 3B2R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B2R contains 41 α-helices and 0 β-strands across 2 chains. 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: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	533-545	13
α-helix	551-554	4
α-helix	568-581	14
α-helix	584-587	4
α-helix	592-604	13
α-helix	607	1
α-helix	615-629	15
α-helix	635-637	3
α-helix	640-652	13
α-helix	678-680	3
α-helix	687-694	8
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-765	17
α-helix	766-769	4
α-helix	772-790	19
α-helix	810-812	3
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

Chain B: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	539-545	7
α-helix	551-554	4
α-helix	568-581	14
α-helix	584-587	4
α-helix	592-604	13
α-helix	615-629	15
α-helix	635-637	3
α-helix	640-652	13
α-helix	687-694	8
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-786	15
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	A, B	protein	330	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3B2R_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A, B)
GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQM
KHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAA
LSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYK
TTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITK
PWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYE
ALTHVSEDCFPLLDGCRKNRQKWQALAEQQ

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	2

Primary citation

Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil. Wang, H., Ye, M., Robinson, H. et al. Mol Pharmacol (2008) 73:104-110. DOI 10.1124/mol.107.040212 · 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
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

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