Structure of PDB 6l6e Chain A Binding Site BS01

Receptor Information
>6l6e Chain A (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLV
QNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQ
NKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHH
FDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEF
FELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATE
FFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHV
SEDCFPLLDGCRKNRQKWQALAEQ
Ligand information
Ligand IDE6L
InChIInChI=1S/C23H26ClN7O3/c1-34-19-6-5-15(10-18(19)24)11-27-21-17(22(33)28-13-20-25-7-3-8-26-20)12-29-23(30-21)31-9-2-4-16(31)14-32/h3,5-8,10,12,16,32H,2,4,9,11,13-14H2,1H3,(H,28,33)(H,27,29,30)/t16-/m0/s1
InChIKeyWEAJZXNPAWBCOA-INIZCTEOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(CNc2nc(ncc2C(=O)NCc3ncccn3)N4CCC[C@H]4CO)cc1Cl
OpenEye OEToolkits 2.0.7COc1ccc(cc1Cl)CNc2c(cnc(n2)N3CCCC3CO)C(=O)NCc4ncccn4
OpenEye OEToolkits 2.0.7COc1ccc(cc1Cl)CNc2c(cnc(n2)N3CCC[C@H]3CO)C(=O)NCc4ncccn4
CACTVS 3.385COc1ccc(CNc2nc(ncc2C(=O)NCc3ncccn3)N4CCC[CH]4CO)cc1Cl
FormulaC23 H26 Cl N7 O3
Name4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid ine-5-carboxamide;
Avanafil
ChEMBLCHEMBL1963681
DrugBankDB06237
ZINCZINC000011677857
PDB chain6l6e Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6l6e 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.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		Y612 L725 Q775 A779 V782 A783 F786 F787 L804 I813 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		Y77 L190 Q240 A244 V247 A248 F251 F252 L269 I278 M281 Q282 F285
Annotation score1
Binding affinityBindingDB: Ki=5.0nM
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0007165 signal transduction

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Molecular Function
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Biological Process
External links
PDB RCSB:6l6e, PDBe:6l6e, PDBj:6l6e
PDBsum6l6e
PubMed32663396
UniProtO76074|PDE5A_HUMAN cGMP-specific 3',5'-cyclic phosphodiesterase (Gene Name=PDE5A)

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