Structure of PDB 6y5c Chain A Binding Site BS01

Receptor Information
>6y5c Chain A (length=809) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNFD
AFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNH
TVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRR
MSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPH
KFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDD
EAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQL
LNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIG
DVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTG
NMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYN
AQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADY
EEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGV
EPSRQRLPA
Ligand information
Ligand IDO9T
InChIInChI=1S/C16H12O4/c1-9-2-4-10(5-3-9)14-8-13(19)16-12(18)6-11(17)7-15(16)20-14/h2-8,17-18H,1H3
InChIKeyPXFZXOXUQVAZOV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1ccc(cc1)C2=CC(=O)c3c(cc(cc3O2)O)O
CACTVS 3.385Cc1ccc(cc1)C2=CC(=O)c3c(O)cc(O)cc3O2
FormulaC16 H12 O4
Name2-(4-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one
ChEMBLCHEMBL182262
DrugBank
ZINCZINC000028360254
PDB chain6y5c 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

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PDB6y5c Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		F285 E382 G612 Y613 F771
Binding residue
(residue number reindexed from 1)		F268 E355 G585 Y586 F744
Annotation score1
Binding affinityMOAD: Ki=21.36uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H350 K541 R542 K547 T649 K653
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:6y5c, PDBe:6y5c, PDBj:6y5c
PDBsum6y5c
PubMed32771768
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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