Structure of PDB 5o52 Chain A Binding Site BS02

Receptor Information
>5o52 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 ID9LE
InChIInChI=1S/C19H21N3O4/c20-15-17(25)16(24)14(9-23)26-18(15)19-21-8-13(22-19)12-6-5-10-3-1-2-4-11(10)7-12/h1-8,14-18,23-25H,9,20H2,(H,21,22)/t14-,15-,16-,17-,18-/m1/s1
InChIKeyVXVNVASERGBQNT-DUQPFJRNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)c3c[nH]c(n3)[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)N
CACTVS 3.385N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1c2[nH]cc(n2)c3ccc4ccccc4c3
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)c3c[nH]c(n3)C4C(C(C(C(O4)CO)O)O)N
CACTVS 3.385N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1c2[nH]cc(n2)c3ccc4ccccc4c3
FormulaC19 H21 N3 O4
Name(2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1~{H}-imidazol-2-yl)oxane-3,4-diol
ChEMBLCHEMBL4101331
DrugBank
ZINC
PDB chain5o52 Chain A Residue 902 [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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PDB5o52 Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		N282 N284 F285 H341 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		N265 N267 F268 H315 H351 N458 E646 S648 G649
Annotation score1
Binding affinityBindingDB: Ki=191nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5o52, PDBe:5o52, PDBj:5o52
PDBsum5o52
PubMed28925695
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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