Structure of PDB 6qa8 Chain A Binding Site BS01

Receptor Information
>6qa8 Chain A (length=806) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDGYIQAVLDRN
LAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNFDAFP
DKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVL
PEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSL
VEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQ
NKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAF
IRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNC
LHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVV
NHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMK
FMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQE
YYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEY
VKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPS
RQRLPA
Ligand information
Ligand IDHTE
InChIInChI=1S/C14H16N2O6/c17-6-8-9(18)10(19)11(20)14(22-8)13(21)15-12(16-14)7-4-2-1-3-5-7/h1-5,8-11,17-20H,6H2,(H,15,16,21)/t8-,9-,10+,11-,14+/m1/s1
InChIKeyBCSCGCOVRJYILO-QEGBUVANSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)C2=NC3(C(C(C(C(O3)CO)O)O)O)C(=O)N2
CACTVS 3.385OC[C@H]1O[C@@]2(N=C(NC2=O)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.6c1ccc(cc1)C2=N[C@]3([C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)C(=O)N2
CACTVS 3.385OC[CH]1O[C]2(N=C(NC2=O)c3ccccc3)[CH](O)[CH](O)[CH]1O
FormulaC14 H16 N2 O6
Name(5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one
ChEMBLCHEMBL4514550
DrugBank
ZINC
PDB chain6qa8 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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PDB6qa8 Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		G135 L136 L139 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 L128 H347 N454 E642 A643 S644 G645
Annotation score1
Binding affinityMOAD: Ki=9uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H347 K538 R539 K544 T646 K650
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:6qa8, PDBe:6qa8, PDBj:6qa8
PDBsum6qa8
PubMed31251604
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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