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BioLiP

Structure of PDB 6f3u Chain A Binding Site BS03

Receptor Information
>6f3u 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 IDCNK
InChIInChI=1S/C18H19N3O5/c22-8-12-13(23)14(24)15(25)16(26-12)18-19-17(20-21-18)11-7-3-5-9-4-1-2-6-10(9)11/h1-7,12-16,22-25H,8H2,(H,19,20,21)/t12-,13-,14+,15-,16-/m1/s1
InChIKeyUGWCMNZLMGJTJS-IBEHDNSVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cccc2c3[nH]c(nn3)C4C(C(C(C(O4)CO)O)O)O
CACTVS 3.385OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2[nH]c(nn2)c3cccc4ccccc34
CACTVS 3.385OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2[nH]c(nn2)c3cccc4ccccc34
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cccc2c3[nH]c(nn3)[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O
FormulaC18 H19 N3 O5
Name(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(5-naphthalen-1-yl-4~{H}-1,2,4-triazol-3-yl)oxane-3,4,5-triol
ChEMBLCHEMBL4164542
DrugBank
ZINC
PDB chain6f3u Chain A Residue 903 [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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PDB6f3u A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		E88 N282 N284 F285 H341 H377 A383 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		E77 N265 N267 F268 H315 H351 A357 N458 E646 S648 G649
Annotation score1
Binding affinityMOAD: Ki=11.5uM
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:6f3u, PDBe:6f3u, PDBj:6f3u
PDBsum6f3u
PubMed29453094
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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