1RKP: PDE5A1-IBMX

Crystal structure of PDE5A1-IBMX. Determined by X-ray diffraction at 2.05 Å resolution. Released 30 Mar 2004.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,673
Mol. weight: 38.1 kDa
Ligands: ZN, MG, IBM
Released: 30 Mar 2004

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

Secondary structure: helices and β-sheets

1RKP contains 22 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: 22 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	615-629	15
α-helix	635-637	3
α-helix	640-652	13
α-helix	664-667	4
α-helix	673-676	4
α-helix	680-694	15
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-783	12
α-helix	784-788	5
α-helix	812-820	9
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	326	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1RKP_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEV
LCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHD
LDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLK
IIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPI
QQRLAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTH
VSEDCFPLLDGCRKNRQKWQALAEQQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
IBM	3-isobutyl-1-methylxanthine	C10 H14 N4 O2	1

Primary citation

Crystal structures of phosphodiesterases 4 and 5 in complex with inhibitor IBMX suggest a conformation determinant of inhibitor selectivity. Huai, Q., Liu, Y., Francis, S.H. et al. J Biol Chem (2004) 279:13095-13101. DOI 10.1074/jbc.M311556200 · 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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