Structure of PDB 3ebo Chain A Binding Site BS01

Receptor Information
>3ebo 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 ID57D
InChIInChI=1S/C15H10O4/c16-10-6-11(17)15-12(18)8-13(19-14(15)7-10)9-4-2-1-3-5-9/h1-8,16-17H
InChIKeyRTIXKCRFFJGDFG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C2=CC(=O)c3c(cc(cc3O2)O)O
CACTVS 3.341Oc1cc(O)c2C(=O)C=C(Oc2c1)c3ccccc3
ACDLabs 10.04O=C1c3c(OC(=C1)c2ccccc2)cc(O)cc3O
FormulaC15 H10 O4
Namechrysin;
5,7-dihydroxy-2-phenyl-4H-chromen-4-one
ChEMBLCHEMBL117
DrugBankDB15581
ZINCZINC000003872070
PDB chain3ebo Chain A Residue 940 [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]
PDB3ebo Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: Comparison of chrysin and flavopiridol
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F285 E382 A610 G612 Y613
Binding residue
(residue number reindexed from 1)		F268 E356 A584 G586 Y587
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.72,Ki=19.01uM
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:3ebo, PDBe:3ebo, PDBj:3ebo
PDBsum3ebo
PubMed23279842
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]