Structure of PDB 6y55 Chain A Binding Site BS01

Receptor Information
>6y55 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 IDO9Q
InChIInChI=1S/C16H12O4/c1-9-3-2-4-10(5-9)14-8-13(19)16-12(18)6-11(17)7-15(16)20-14/h2-8,17-18H,1H3
InChIKeyIGTBSDZAEVYRPZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cccc(c1)C2=CC(=O)c3c(O)cc(O)cc3O2
OpenEye OEToolkits 2.0.7Cc1cccc(c1)C2=CC(=O)c3c(cc(cc3O2)O)O
FormulaC16 H12 O4
Name2-(3-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one
ChEMBLCHEMBL3781227
DrugBank
ZINCZINC000653729309
PDB chain6y55 Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6y55 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.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		N284 F285 E382 A610 G612 Y613 R770
Binding residue
(residue number reindexed from 1)		N267 F268 E355 A583 G585 Y586 R743
Annotation score1
Binding affinityMOAD: Ki=2.23uM
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:6y55, PDBe:6y55, PDBj:6y55
PDBsum6y55
PubMed32771768
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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