Structure of PDB 3ebp Chain A Binding Site BS01

Receptor Information
>3ebp 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 IDCPB
InChIInChI=1S/C21H20ClNO5/c1-23-7-6-12(17(27)10-23)19-14(24)8-15(25)20-16(26)9-18(28-21(19)20)11-4-2-3-5-13(11)22/h2-5,8-9,12,17,24-25,27H,6-7,10H2,1H3/t12-,17+/m0/s1
InChIKeyBIIVYFLTOXDAOV-YVEFUNNKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN1CCC(C(C1)O)c2c(cc(c3c2OC(=CC3=O)c4ccccc4Cl)O)O
ACDLabs 10.04Clc4ccccc4C=2Oc1c(c(O)cc(O)c1C(=O)C=2)C3CCN(C)CC3O
OpenEye OEToolkits 1.5.0C[N@]1CC[C@@H]([C@@H](C1)O)c2c(cc(c3c2OC(=CC3=O)c4ccccc4Cl)O)O
CACTVS 3.341CN1CC[CH]([CH](O)C1)c2c(O)cc(O)c3C(=O)C=C(Oc23)c4ccccc4Cl
CACTVS 3.341CN1CC[C@@H]([C@H](O)C1)c2c(O)cc(O)c3C(=O)C=C(Oc23)c4ccccc4Cl
FormulaC21 H20 Cl N O5
Name2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE;
FLAVOPIRIDOL
ChEMBLCHEMBL428690
DrugBankDB03496
ZINCZINC000021288966
PDB chain3ebp 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

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PDB3ebp 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
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N284 F285 L380 E382 A610 G612 Y613
Binding residue
(residue number reindexed from 1)		N267 F268 L354 E356 A584 G586 Y587
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.91,Ki=1.24uM
BindingDB: IC50=1200nM
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:3ebp, PDBe:3ebp, PDBj:3ebp
PDBsum3ebp
PubMed23279842
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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