Structure of PDB 6s4h Chain A Binding Site BS01

Receptor Information
>6s4h 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 IDKUQ
InChIInChI=1S/C15H18N2O5/c18-7-10-11(19)12(20)13(21)14(22-10)9-6-16-15(17-9)8-4-2-1-3-5-8/h1-6,10-14,18-21H,7H2,(H,16,17)/t10-,11-,12+,13-,14+/m1/s1
InChIKeyHSTOUPNMEGVFOM-RGDJUOJXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)c2[nH]cc(n2)C3C(C(C(C(O3)CO)O)O)O
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2c[nH]c(n2)c3ccccc3
OpenEye OEToolkits 2.0.7c1ccc(cc1)c2[nH]cc(n2)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2c[nH]c(n2)c3ccccc3
FormulaC15 H18 N2 O5
Name(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-phenyl-1~{H}-imidazol-4-yl)oxane-3,4,5-triol
ChEMBLCHEMBL4638064
DrugBank
ZINC
PDB chain6s4h 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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PDB6s4h The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 N284 H341 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N265 N267 H315 H351 N458 E646 S648 G649
Annotation score1
Binding affinityMOAD: Ki=68.6uM
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:6s4h, PDBe:6s4h, PDBj:6s4h
PDBsum6s4h
PubMed31767404
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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