Structure of PDB 5u00 Chain A Binding Site BS01

Receptor Information
>5u00 Chain A (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQD
MNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNL
ELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSV
MERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLR
IFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAEL
IYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQ
DLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL
Ligand information
Ligand ID7OV
InChIInChI=1S/C18H15F3IN5O/c1-10-4-15(27-17(25-10)23-9-24-27)12-6-18(20,21)8-26(7-12)16(28)11-2-3-13(19)14(22)5-11/h2-5,9,12H,6-8H2,1H3/t12-/m0/s1
InChIKeyBCKWAMYDZGLZLN-LBPRGKRZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(n2c(n1)ncn2)C3CC(CN(C3)C(=O)c4ccc(c(c4)I)F)(F)F
CACTVS 3.385Cc1cc([CH]2CN(CC(F)(F)C2)C(=O)c3ccc(F)c(I)c3)n4ncnc4n1
ACDLabs 12.01n4c1ncnn1c(C3CC(F)(CN(C(c2cc(c(F)cc2)I)=O)C3)F)cc4C
OpenEye OEToolkits 2.0.6Cc1cc(n2c(n1)ncn2)[C@H]3CC(CN(C3)C(=O)c4ccc(c(c4)I)F)(F)F
CACTVS 3.385Cc1cc([C@@H]2CN(CC(F)(F)C2)C(=O)c3ccc(F)c(I)c3)n4ncnc4n1
FormulaC18 H15 F3 I N5 O
Name[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](4-fluoro-3-iodophenyl)methanone
ChEMBL
DrugBank
ZINCZINC000584905348
PDB chain5u00 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5u00 Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.
Resolution1.41 Å
Binding residue
(original residue number in PDB)		H656 L770 L809 Q812 I826 Y827 F830 M847 Q859 F862
Binding residue
(residue number reindexed from 1)		H81 L195 L234 Q237 I251 Y252 F255 M272 Q284 F287
Annotation score1
Binding affinityMOAD: ic50=0.002uM
PDBbind-CN: -logKd/Ki=8.70,IC50=0.002uM
BindingDB: IC50=2nM
Enzymatic activity
Enzyme Commision number 3.1.4.17: 3',5'-cyclic-nucleotide 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:5u00, PDBe:5u00, PDBj:5u00
PDBsum5u00
PubMed28165743
UniProtO00408|PDE2A_HUMAN cGMP-dependent 3',5'-cyclic phosphodiesterase (Gene Name=PDE2A)

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