Structure of PDB 4gpb Chain A Binding Site BS01

Receptor Information
>4gpb Chain A (length=833) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACD
EATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGI
RYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHT
SQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNV
GGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIR
RFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERL
DWDKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQR
FLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIH
SEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGE
EYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINP
NSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKA
APGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPA
ADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFF
IFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFK
DIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSG
KFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
Ligand information
Ligand IDGFP
InChIInChI=1S/C6H12FO8P/c7-3-5(10)4(9)2(1-8)14-6(3)15-16(11,12)13/h2-6,8-10H,1H2,(H2,11,12,13)/t2-,3-,4-,5-,6-/m1/s1
InChIKeyLXEHNDWFCMGWAY-QZABAPFNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)OP(=O)(O)O)F)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)O)F)O)O)O
CACTVS 3.341OC[C@H]1O[C@H](O[P](O)(O)=O)[C@H](F)[C@@H](O)[C@@H]1O
CACTVS 3.341OC[CH]1O[CH](O[P](O)(O)=O)[CH](F)[CH](O)[CH]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1F)CO)(O)O
FormulaC6 H12 F O8 P
Name2-deoxy-2-fluoro-1-O-phosphono-alpha-D-glucopyranose;
2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-PHOSPHATE;
2-deoxy-2-fluoro-1-O-phosphono-alpha-D-glucose;
2-deoxy-2-fluoro-1-O-phosphono-D-glucose;
2-deoxy-2-fluoro-1-O-phosphono-glucose
ChEMBLCHEMBL1233022
DrugBank
ZINCZINC000005830076
PDB chain4gpb Chain A Residue 900 [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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PDB4gpb Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G135 L136 N284 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G126 L127 N275 H368 N475 E663 A664 S665 G666
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H368 K559 R560 K565 T667 K671
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4gpb, PDBe:4gpb, PDBj:4gpb
PDBsum4gpb
PubMed2125493
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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