Structure of PDB 1gpy Chain A Binding Site BS01

Receptor Information
>1gpy Chain A (length=828) 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
KWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYI
QAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKS
SKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDK
AWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNR
VAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEIL
KKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYIS
DLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLF
DVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGY
HMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLS
EQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGM
RVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVN
MLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSS
DRTIAQYAREIWGVEPSRQRLPAPDEKI
Ligand information
Ligand IDG6P
InChIInChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6+/m1/s1
InChIKeyNBSCHQHZLSJFNQ-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)OP(=O)(O)O
CACTVS 3.341O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@H]1O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC1OC(O)C(O)C(O)C1O
FormulaC6 H13 O9 P
Name6-O-phosphono-alpha-D-glucopyranose;
ALPHA-D-GLUCOSE-6-PHOSPHATE;
6-O-phosphono-alpha-D-glucose;
6-O-phosphono-D-glucose;
6-O-phosphono-glucose
ChEMBL
DrugBankDB02007
ZINCZINC000003875375
PDB chain1gpy 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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PDB1gpy Crystallographic binding studies on the allosteric inhibitor glucose-6-phosphate to T state glycogen phosphorylase b.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I68 R193 D227 R242 R309 R310
Binding residue
(residue number reindexed from 1)		I55 R180 D214 R229 R296 R297
Annotation score2
Binding affinityMOAD: Kd~25uM
PDBbind-CN: -logKd/Ki=4.70,Kd=20uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H364 K555 R556 K561 T663 K667
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:1gpy, PDBe:1gpy, PDBj:1gpy
PDBsum1gpy
PubMed8331662
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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