3BJC: PDE5A catalytic domain

Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor. Determined by X-ray diffraction at 2.0 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,665
Mol. weight: 100.91 kDa
Ligands: WAN, MG, ZN
Released: 29 Apr 2008

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

Secondary structure: helices and β-sheets

3BJC contains 21 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: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	537-545	9
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	665-667	3
α-helix	673-676	4
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	772-787	16
α-helix	809-820	12
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	protein	878	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BJC_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
GSHMERAGPSFGQQRQQQQPQQQKQQQRDQDSVEAWLDDHWDFTFSYFVRKATREMVNAW
FAERVHTIPVCKEGIRGHTESCSCPLQQSPRADNSVPGTPTRKISASEFDRPLRPIVVKD
SEGTVSFLSDSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIH
GLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALG
EPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTE
KDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAAT
IISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKN
TMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEEN
TGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKQMVTLEVLSYHASAAEEET
RELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCR
WILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDH
RGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIK
QAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQR
IAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSE
DCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN

Ligands and cofactors

ID	Name	Formula	Copies
WAN	5-ethoxy-4-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-y…	C15 H19 N5 O4 S2	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Primary citation

An insight into the pharmacophores of phosphodiesterase-5 inhibitors from synthetic and crystal structural studies. Chen, G., Wang, H., Robinson, H. et al. Biochem Pharmacol (2008) 75:1717-1728. DOI 10.1016/j.bcp.2008.01.019 · 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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