Structure of PDB 4ej2 Chain A Binding Site BS01

Receptor Information
>4ej2 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 IDD1F
InChIInChI=1S/C17H24N2O7/c1-2-3-4-5-6-7-10-8-19(17(25)18-15(10)24)16-14(23)13(22)12(21)11(9-20)26-16/h8,11-14,16,20-23H,2-5,9H2,1H3,(H,18,24,25)/t11-,12-,13+,14-,16-/m1/s1
InChIKeyZIAKFTYLGUACKB-XYFZXANASA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCC#CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CCCCCC#CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O
OpenEye OEToolkits 1.7.6CCCCCC#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.370CCCCCC#CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O
ACDLabs 12.01O=C1NC(=O)N(C=C1C#CCCCCC)C2OC(C(O)C(O)C2O)CO
FormulaC17 H24 N2 O7
Name1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL2041077
DrugBank
ZINCZINC000084738787
PDB chain4ej2 Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ej2 The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 D339 T340 H377 A383 L384 E385 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D266 D313 T314 H351 A357 L358 E359 N458 E646 A647 S648 G649
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.49,Ki=3204uM
BindingDB: IC50=6100000nM
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:4ej2, PDBe:4ej2, PDBj:4ej2
PDBsum4ej2
PubMed22770609
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]