Structure of PDB 6qa6 Chain A Binding Site BS01

Receptor Information
>6qa6 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 IDHT8
InChIInChI=1S/C18H18N2O6/c21-8-12-13(22)14(23)15(24)18(26-12)17(25)19-16(20-18)11-6-5-9-3-1-2-4-10(9)7-11/h1-7,12-15,21-24H,8H2,(H,19,20,25)/t12-,13-,14+,15-,18+/m1/s1
InChIKeyQSYAFZZRALZDHF-NSIVTLKISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)C3=NC4(C(C(C(C(O4)CO)O)O)O)C(=O)N3
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)C3=N[C@]4([C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)C(=O)N3
CACTVS 3.385OC[CH]1O[C]2(N=C(NC2=O)c3ccc4ccccc4c3)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@@]2(N=C(NC2=O)c3ccc4ccccc4c3)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC18 H18 N2 O6
Name(5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one
ChEMBLCHEMBL4514774
DrugBank
ZINC
PDB chain6qa6 Chain A Residue 1102 [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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PDB6qa6 Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 N284 H341 H377 T378 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N265 N267 H315 H351 T352 N458 E646 A647 S648 G649
Annotation score1
Binding affinityMOAD: Ki=2.11uM
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
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Biological Process
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Cellular Component
External links
PDB RCSB:6qa6, PDBe:6qa6, PDBj:6qa6
PDBsum6qa6
PubMed31251604
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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