Structure of PDB 8syc Chain D Binding Site BS02

Receptor Information
>8syc Chain D (length=355) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VEEYDSLIEKMSNWNFPIFELVEKMGEDSGRILSQVMYTLFQDTGLLEIF
KIPTQQFMNYFRALENGYRDIPYHNRIHATDVLHAVWYLTTRPVPGLQQI
HIAYISSKSCSNPDESYGCLSSNIPALELMALYVAAAMHDYDHPGRTNEF
LVATNAPQAVLYNDRSVLENHHAASAWNLYLSRPEYNFLLHLDHVEFERF
RFLVIEAILATDLKKHFDFLAEFNAKANDVNSNGIEWSNENDRLLVCQVC
IKLADINGPAKVRDLHLKWTEGIVNEFYEQGDEEANLGLPISPFMDRSDP
QLAKLQESFITHIVGPLCNSYDAAGLLPGQWLRIFCQLMHHLTENHKIWK
ENLYF
Ligand information
Ligand IDX5W
InChIInChI=1S/C27H25BN3O6/c1-31(16-17-7-5-4-6-8-17)27(33)18-11-19(28(34)35)13-20(12-18)29-26(32)24-15-25(37-3)22-10-9-21(36-2)14-23(22)30-24/h4-15,34H,16H2,1-3H3,(H,29,32)
InChIKeyZSCFNVNMTWBBBO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc2c(OC)cc(nc2c1)C(=O)Nc3cc(cc(c3)C(=O)N(C)Cc4ccccc4)[B](O)=O
OpenEye OEToolkits 2.0.7B(=O)(c1cc(cc(c1)NC(=O)c2cc(c3ccc(cc3n2)OC)OC)C(=O)N(C)Cc4ccccc4)O
FormulaC27 H25 B N3 O6
Name[3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron
ChEMBL
DrugBank
ZINC
PDB chain8syc Chain D Residue 1103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8syc Discovery and SAR Study of Boronic Acid-Based Selective PDE3B Inhibitors from a Novel DNA-Encoded Library.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y736 H737 D822 H825 G940 W951 I955 F959 L987 Q988 F991
Binding residue
(residue number reindexed from 1)		Y73 H74 D140 H143 G258 W269 I273 F277 L305 Q306 F309
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8syc, PDBe:8syc, PDBj:8syc
PDBsum8syc
PubMed38284310
UniProtQ13370|PDE3B_HUMAN cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B (Gene Name=PDE3B)

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