Structure of PDB 2pri Chain A Binding Site BS01

Receptor Information
>2pri Chain A (length=830) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDH
LVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEAT
YQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYE
FGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQG
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGY
IQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFK
SSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWD
KAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLN
RVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEI
LKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYI
SDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSL
FDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPG
YHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADL
SEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFG
MRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIV
NMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFS
SDRTIAQYAREIWGVEPSRQRLPAPDEKIP
Ligand information
Ligand IDD6G
InChIInChI=1S/C6H13O8P/c7-3-1-5(8)14-4(6(3)9)2-13-15(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4-,5+,6+/m1/s1
InChIKeyUQJFZAAGZAYVKZ-ZXXMMSQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1[C@H]([C@@H]([C@H](O[C@@H]1O)COP(=O)(O)O)O)O
CACTVS 3.370O[CH]1C[CH](O)[CH](O)[CH](CO[P](O)(O)=O)O1
ACDLabs 12.01O=P(O)(O)OCC1OC(O)CC(O)C1O
OpenEye OEToolkits 1.7.6C1C(C(C(OC1O)COP(=O)(O)O)O)O
CACTVS 3.370O[C@@H]1C[C@@H](O)[C@H](O)[C@@H](CO[P](O)(O)=O)O1
FormulaC6 H13 O8 P
Name2-deoxy-6-O-phosphono-alpha-D-glucopyranose;
2-deoxy-6-O-phosphono-alpha-D-arabino-hexopyranose;
2-deoxy-alpha-D-glucopyranose 6-phosphate;
2-deoxy-6-O-phosphono-alpha-D-glucose;
2-deoxy-6-O-phosphono-D-glucose;
2-deoxy-6-O-phosphono-glucose
ChEMBL
DrugBank
ZINCZINC000004097095
PDB chain2pri Chain A Residue 930 [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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PDB2pri The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		W67 Y75 R193 D227 R310
Binding residue
(residue number reindexed from 1)		W55 Y63 R181 D215 R298
Annotation score1
Binding affinityMOAD: Ki=1.23mM
PDBbind-CN: -logKd/Ki=2.91,Ki=1.23mM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H365 K556 R557 K562 T664 K668
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:2pri, PDBe:2pri, PDBj:2pri
PDBsum2pri
PubMed7500360
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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