Structure of PDB 3bd7 Chain A Binding Site BS02

Receptor Information
>3bd7 Chain A (length=810) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRD
HLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEA
TYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQ
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA
Ligand information
Ligand IDCKB
InChIInChI=1S/C11H16N2O7/c1-4-2-13(11(19)12-9(4)18)10-8(17)7(16)6(15)5(3-14)20-10/h2,5-8,10,14-17H,3H2,1H3,(H,12,18,19)/t5-,6-,7+,8-,10-/m1/s1
InChIKeyRMXUFBPORJBBEZ-HPFNVAMJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O
CACTVS 3.341CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.341CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C(O)C2O)CO
FormulaC11 H16 N2 O7
Name1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione;
1-D-glucopyranosyl-thymine;
1-beta-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione;
1-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione;
1-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL1231802
DrugBank
ZINCZINC000038274401
PDB chain3bd7 Chain A Residue 940 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bd7 D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F285 G612 Y613
Binding residue
(residue number reindexed from 1)		F268 G586 Y587
Annotation score1
Binding affinityBindingDB: IC50=6600nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H351 K542 R543 K548 T650 K654
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:3bd7, PDBe:3bd7, PDBj:3bd7
PDBsum3bd7
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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