Structure of PDB 1pyg Chain B Binding Site BS01

Receptor Information
>1pyg Chain B (length=791) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIR
TQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDM
EELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQK
ICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQ
VVLAMPYDTPVPGYRNNVVNTMRLWSAKAPQAVLDRNLAENISKELRLKQ
EYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLA
IPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETL
LPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLC
IAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLC
NPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKF
AAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPN
KFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFL
ENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGA
NVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQL
SSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPR
EWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPA
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain1pyg Chain A Residue 843 [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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PDB1pyg Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		D42 N44 V45
Binding residue
(residue number reindexed from 1)		D23 N25 V26
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.52,Kd=3uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H332 K523 R524 K529 T631 K635
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:1pyg, PDBe:1pyg, PDBj:1pyg
PDBsum1pyg
PubMed1962195
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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