Structure of PDB 1xkx Chain A Binding Site BS01

Receptor Information
>1xkx 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 IDIMK
InChIInChI=1S/C14H18N2O5/c1-6-2-3-7-8(4-6)16-14(15-7)13-12(20)11(19)10(18)9(5-17)21-13/h2-4,9-13,17-20H,5H2,1H3,(H,15,16)/t9-,10-,11+,12-,13-/m1/s1
InChIKeyXIJZORUYQZBFJK-UJPOAAIJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1ccc2c(c1)nc([nH]2)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
CACTVS 3.370Cc1ccc2[nH]c(nc2c1)[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O
ACDLabs 12.01OC1C(O)C(O)C(OC1CO)c3nc2cc(ccc2n3)C
OpenEye OEToolkits 1.7.6Cc1ccc2c(c1)nc([nH]2)C3C(C(C(C(O3)CO)O)O)O
CACTVS 3.370Cc1ccc2[nH]c(nc2c1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
FormulaC14 H18 N2 O5
Name2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1-BENZIMIDAZOLE;
2-(BETA-D-GLUCOPYRANOSYL)-5-METHYL-1,2,3-BENZIMIDAZOLE
ChEMBL
DrugBankDB03133
ZINCZINC000038378584
PDB chain1xkx Chain A Residue 910 [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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PDB1xkx Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site
Resolution1.93 Å
Binding residue
(original residue number in PDB)		Y203 Q219 V221 K294
Binding residue
(residue number reindexed from 1)		Y192 Q208 V210 K277
Annotation score1
Binding affinityMOAD: Ki=8.6uM
BindingDB: Ki=9000nM,IC50=8600nM
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:1xkx, PDBe:1xkx, PDBj:1xkx
PDBsum1xkx
PubMed15741340
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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