Structure of PDB 3hmv Chain A Binding Site BS02

Receptor Information
>3hmv Chain A (length=351) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQ
ERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLS
TPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDES
VLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHM
SLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLE
LYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIV
HPLWETWADLVQPDAQDILDTLEDNRNWYQAMIPQNRDCQGLMEKFQFEL
T
Ligand information
Ligand IDHBT
InChIInChI=1S/C17H17N3O4S/c1-9-6-7-11-13(8-9)25-17(14(11)15(18)21)19-16(22)10-4-2-3-5-12(10)20(23)24/h2-5,9H,6-8H2,1H3,(H2,18,21)(H,19,22)/t9-/m0/s1
InChIKeyOBHKTNMETRQPKN-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1CCc2c(sc(c2C(=O)N)NC(=O)c3ccccc3[N+](=O)[O-])C1
CACTVS 3.341C[C@H]1CCc2c(C1)sc(NC(=O)c3ccccc3[N+]([O-])=O)c2C(N)=O
CACTVS 3.341C[CH]1CCc2c(C1)sc(NC(=O)c3ccccc3[N+]([O-])=O)c2C(N)=O
OpenEye OEToolkits 1.5.0C[C@H]1CCc2c(sc(c2C(=O)N)NC(=O)c3ccccc3[N+](=O)[O-])C1
ACDLabs 10.04[O-][N+](=O)c1ccccc1C(=O)Nc2sc3c(c2C(=O)N)CCC(C3)C
FormulaC17 H17 N3 O4 S
Name(6S)-6-methyl-2-{[(2-nitrophenyl)carbonyl]amino}-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000000687045
PDB chain3hmv Chain A Residue 530 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3hmv Identification of PDE4B Over 4D subtype-selective inhibitors revealing an unprecedented binding mode
Resolution2.23 Å
Binding residue
(original residue number in PDB)		M347 D392 N395 Y403 I410 M411 F414 Q443 F446
Binding residue
(residue number reindexed from 1)		M196 D241 N244 Y252 I259 M260 F263 Q292 F295
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,IC50=50.12nM
BindingDB: IC50=50nM
Enzymatic activity
Enzyme Commision number 3.1.4.53: 3',5'-cyclic-AMP 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:3hmv, PDBe:3hmv, PDBj:3hmv
PDBsum3hmv
PubMed19525117
UniProtQ07343|PDE4B_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4B (Gene Name=PDE4B)

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