4I9Z: PDE5A1 catalytic domain

Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors. Determined by X-ray diffraction at 2.08 Å resolution. Released 1 Jan 2014.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,572
Mol. weight: 40.88 kDa
Ligands: 5BA, MG, ZN
Released: 1 Jan 2014

Explore 4I9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4I9Z contains 19 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: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	536-545	10
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	680-693	14
α-helix	706-721	16
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	840-856	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cGMP-specific 3',5'-cyclic phosphodiesterase	A	protein	347	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4I9Z_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
MGSSHHHHHHSSGLVPRGSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETAL
CTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGK
IQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMIL
NSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKE
LFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKI
PSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ

Ligands and cofactors

ID	Name	Formula	Copies
5BA	5-bromo-2-{5-[(4-methylpiperazin-1-yl)acetyl]-2-propoxyphenyl}-6-(propan-2-yl)p…	C23 H31 Br N4 O3	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5. Gong, X., Wang, G., Ren, J. et al. Bioorg Med Chem Lett (2013) 23:4944-4947. DOI 10.1016/j.bmcl.2013.06.062 · 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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