1UDT: Human Phosphodiesterase 5

Crystal structure of Human Phosphodiesterase 5 complexed with Sildenafil(Viagra). Determined by X-ray diffraction at 2.3 Å resolution. Released 11 May 2004.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,655
Mol. weight: 38.09 kDa
Ligands: ZN, VIA, MG
Released: 11 May 2004

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

Secondary structure: helices and β-sheets

1UDT contains 21 α-helices and 2 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: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	538-545	8
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	680-694	15
β-strand	702	1	1
β-strand	704	1	1
α-helix	706-722	17
α-helix	725-741	17
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-796	25
α-helix	800-802	3
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	840-859	20

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>1UDT_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLC
RWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLD
HRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKII
KQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQ
RIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVS
EDCFPLLDGCRKNRQKWQALAEQQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
VIA	5-{2-ethoxy-5-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-1-methyl-3-propyl-1H,6H…	C22 H30 N6 O4 S	1
MG	Magnesium ion	Mg	1

Primary citation

Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules. Sung, B.-J., Hwang, K.Y., Jeon, Y.H. et al. Nature (2003) 425:98-102. DOI 10.1038/nature01914 · 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

Browse more

1UDT is part of these collections:

Drugs bound to their targets

About this viewer

MolViewer shows 1UDT 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.