Structure of PDB 2g9u Chain A Binding Site BS02

Receptor Information
>2g9u Chain A (length=803) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHL
VGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATY
QLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEF
GIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGA
KWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVLDR
NLAENISRVLYPNGKELRLKQEYFVVAATLQDIIRRFKSSTNFDAFPDKV
AIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEA
LERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEE
GAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKT
NGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRD
VAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHV
ITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHD
PVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFML
NGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYD
RIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKC
QERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQR
LPA
Ligand information
Ligand IDG27
InChIInChI=1S/C15H23NO3/c17-11-13-9-16(10-14(18)15(13)19)8-4-7-12-5-2-1-3-6-12/h1-3,5-6,13-15,17-19H,4,7-11H2/t13-,14-,15-/m1/s1
InChIKeyNKARZGURZMIRMA-RBSFLKMASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCC[N@@]2C[C@@H]([C@H]([C@@H](C2)O)O)CO
ACDLabs 10.04OCC2CN(CCCc1ccccc1)CC(O)C2O
CACTVS 3.341OC[C@H]1CN(CCCc2ccccc2)C[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0c1ccc(cc1)CCCN2CC(C(C(C2)O)O)CO
CACTVS 3.341OC[CH]1CN(CCCc2ccccc2)C[CH](O)[CH]1O
FormulaC15 H23 N O3
Name(3R,4R,5R)-5-(HYDROXYMETHYL)-1-(3-PHENYLPROPYL)PIPERIDINE-3,4-DIOL
ChEMBLCHEMBL213661
DrugBankDB07807
ZINCZINC000024805808
PDB chain2g9u Chain A Residue 998 [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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PDB2g9u Iminosugars as potential inhibitors of glycogenolysis: structural insights into the molecular basis of glycogen phosphorylase inhibition.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		H377 N484 R569 H571 E672 S674 G675
Binding residue
(residue number reindexed from 1)		H344 N451 R536 H538 E639 S641 G642
Annotation score1
Binding affinityMOAD: ic50=0.84uM
PDBbind-CN: -logKd/Ki=6.08,IC50=0.84uM
BindingDB: IC50=840nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H344 K535 R536 K541 T643 K647
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0008184 glycogen phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0098723 skeletal muscle myofibril

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2g9u, PDBe:2g9u, PDBj:2g9u
PDBsum2g9u
PubMed16970395
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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