6L6E: Human PDE5 catalytic core

Human PDE5 catalytic core in complex with avanafil. Determined by X-ray diffraction at 1.92 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,730
Mol. weight: 39.66 kDa
Ligands: E6L, ZN, MG
Released: 2 Sept 2020

Explore 6L6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L6E contains 24 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: 24 helices, 0 β-strands

Element	Residues	Length
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	634-637	4
α-helix	640-652	13
α-helix	662-667	6
α-helix	672-675	4
α-helix	680-693	14
α-helix	706-722	17
α-helix	725-741	17
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-797	26
α-helix	800-802	3
α-helix	803-805	3
α-helix	807-812	6
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	protein	335	Homo sapiens	O76074 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6L6E_1 cGMP-specific 3',5'-cyclic phosphodiesterase (chains A)
METRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEV
LCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHD
LDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLK
IIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPI
QQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTH
VSEDCFPLLDGCRKNRQKWQALAEQQELEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
E6L	4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolid…	C23 H26 Cl N7 O3	1
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of Human Phosphodiesterase 5A1 Complexed with Avanafil Reveals Molecular Basis of Isoform Selectivity and Guidelines for Targeting alpha-Helix Backbone Oxygen by Halogen Bonding. Hsieh, C.M., Chen, C.Y., Chern, J.W. et al. J Med Chem (2020) 63:8485-8494. DOI 10.1021/acs.jmedchem.0c00853 · 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
3SIE 1.93 Å, Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

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