Structure of PDB 3bda Chain A Binding Site BS03

Receptor Information
>3bda 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 IDC4B
InChIInChI=1S/C9H13N3O8/c13-1-2-3(14)4(15)5(16)6(20-2)12-8(18)10-7(17)11-9(12)19/h2-6,13-16H,1H2,(H2,10,11,17,18,19)/t2-,3-,4+,5-,6-/m1/s1
InChIKeyAWNGSFAGXKOIML-VFUOTHLCSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1N(C(=O)NC(=O)N1)C2OC(C(O)C(O)C2O)CO
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)N2C(=O)NC(=O)NC2=O)O)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)N2C(=O)NC(=O)NC2=O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C(=O)NC(=O)NC2=O
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C(=O)NC(=O)NC2=O
FormulaC9 H13 N3 O8
Name1-beta-D-glucopyranosyl-1,3,5-triazinane-2,4,6-trione;
1-beta-D-glucosyl-1,3,5-triazinane-2,4,6-trione;
1-D-glucosyl-1,3,5-triazinane-2,4,6-trione;
1-glucosyl-1,3,5-triazinane-2,4,6-trione
ChEMBL
DrugBank
ZINCZINC000039040549
PDB chain3bda Chain A Residue 998 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bda D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G135 L136 N284 H377 T378 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N267 H351 T352 N458 E646 S648 G649
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bda, PDBe:3bda, PDBj:3bda
PDBsum3bda
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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