Structure of PDB 3bd6 Chain A Binding Site BS01

Receptor Information
>3bd6 Chain A (length=813) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFG
TNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCA
YTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVD
RLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYE
LEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLS
YVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEY
KRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLI
TAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEA
SGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQ
RGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKV
FADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYARE
IWGVEPSRQRLPA
Ligand information
Ligand IDRDD
InChIInChI=1S/C8H11N3O7/c12-1-2-3(13)4(14)5(18-2)11-7(16)9-6(15)10-8(11)17/h2-5,12-14H,1H2,(H2,9,10,15,16,17)/t2-,3-,4-,5-/m1/s1
InChIKeyDKOBRNXETUUICC-TXICZTDVSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O)N2C(=O)NC(=O)NC2=O
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)N2C(=O)NC(=O)NC2=O)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C(=O)NC(=O)NC2=O)O)O)O
ACDLabs 10.04O=C1N(C(=O)NC(=O)N1)C2OC(C(O)C2O)CO
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C(=O)NC(=O)NC2=O
FormulaC8 H11 N3 O7
Name1-beta-D-ribofuranosyl-1,3,5-triazinane-2,4,6-trione
ChEMBL
DrugBank
ZINC
PDB chain3bd6 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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PDB3bd6 D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y75 R242 R309 R310
Binding residue
(residue number reindexed from 1)		Y64 R231 R292 R293
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H354 K545 R546 K551 T653 K657
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bd6, PDBe:3bd6, PDBj:3bd6
PDBsum3bd6
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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