Structure of PDB 5o56 Chain A Binding Site BS02

Receptor Information
>5o56 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 ID9L8
InChIInChI=1S/C18H20N4O4/c19-13-15(25)14(24)12(8-23)26-16(13)18-20-17(21-22-18)11-6-5-9-3-1-2-4-10(9)7-11/h1-7,12-16,23-25H,8,19H2,(H,20,21,22)/t12-,13-,14-,15-,16-/m1/s1
InChIKeyIMNCDLXOKIGZHY-OXGONZEZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1c2[nH]nc(n2)c3ccc4ccccc4c3
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)c3nc([nH]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]nc(n2)c3ccc4ccccc4c3
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)c3nc([nH]n3)C4C(C(C(C(O4)CO)O)O)N
FormulaC18 H20 N4 O4
Name(2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4-diol
ChEMBLCHEMBL4068103
DrugBank
ZINC
PDB chain5o56 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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PDB5o56 Nanomolar Inhibitors of Glycogen Phosphorylase Based on beta-d-Glucosaminyl Heterocycles: A Combined Synthetic, Enzyme Kinetic, and Protein Crystallography Study.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		L139 N282 N284 F285 R292 H341 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		L128 N265 N267 F268 R275 H315 H351 N458 E646 A647 S648 G649
Annotation score1
Binding affinityBindingDB: Ki=4800nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5o56, PDBe:5o56, PDBj:5o56
PDBsum5o56
PubMed28925695
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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