Structure of PDB 1nok Chain A Binding Site BS02

Receptor Information
>1nok Chain A (length=831) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGG
YIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRF
KSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDW
DKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFL
NRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSE
ILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEY
ISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNS
LFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKPAP
GYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAAD
LSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIF
GMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDI
VNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKF
SSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
Ligand information
Ligand IDNTZ
InChIInChI=1S/C6H10N4O4/c11-1-2-3(12)4(13)5(14)6-7-8-9-10(2)6/h2-5,11-14H,1H2/t2-,3-,4+,5-/m1/s1
InChIKeyUCJXQRFJERKPOZ-SQOUGZDYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H](c2n1nnn2)O)O)O)O
CACTVS 3.341OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)c2nnnn12
ACDLabs 10.04n1nnn2c1C(O)C(O)C(O)C2CO
OpenEye OEToolkits 1.5.0C(C1C(C(C(c2n1nnn2)O)O)O)O
CACTVS 3.341OC[CH]1[CH](O)[CH](O)[CH](O)c2nnnn12
FormulaC6 H10 N4 O4
NameNOJIRIMYCINE TETRAZOLE
ChEMBL
DrugBankDB02471
ZINCZINC000017193216
PDB chain1nok Chain A Residue 998 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1nok Ternary complex crystal structures of glycogen phosphorylase with the transition state analogue nojirimycin tetrazole and phosphate in the T and R states.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G135 L136 L139 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 L128 H366 N473 E661 S663 G664
Annotation score1
Binding affinityMOAD: Ki=700uM
PDBbind-CN: -logKd/Ki=3.15,Ki=700uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H366 K557 R558 K563 T665 K669
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:1nok, PDBe:1nok, PDBj:1nok
PDBsum1nok
PubMed8652510
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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