Structure of PDB 3np9 Chain A Binding Site BS01

Receptor Information
>3np9 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 IDZ2T
InChIInChI=1S/C13H17ClO7/c1-20-5-2-6(9(16)7(14)3-5)13-12(19)11(18)10(17)8(4-15)21-13/h2-3,8,10-13,15-19H,4H2,1H3/t8-,10-,11+,12-,13+/m1/s1
InChIKeyMBLREHINSXJTTD-ZMHPAJMFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0COc1cc(c(c(c1)Cl)O)C2C(C(C(C(O2)CO)O)O)O
OpenEye OEToolkits 1.7.0COc1cc(c(c(c1)Cl)O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.370COc1cc(Cl)c(O)c(c1)[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O
ACDLabs 12.01Clc1cc(OC)cc(c1O)C2OC(CO)C(O)C(O)C2O
CACTVS 3.370COc1cc(Cl)c(O)c(c1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
FormulaC13 H17 Cl O7
Name(1S)-1,5-anhydro-1-(3-chloro-2-hydroxy-5-methoxyphenyl)-D-glucitol
ChEMBLCHEMBL1738940
DrugBank
ZINCZINC000066156452
PDB chain3np9 Chain A Residue 998 [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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PDB3np9 Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: synthesis, enzymatic evaluation and their binding to glycogen phosphorylase.
Resolution1.999 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 N284 D339 H377 T378 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D266 N267 D313 H351 T352 N458 E646 S648 G649
Annotation score1
Binding affinityMOAD: ic50=39.8uM
PDBbind-CN: -logKd/Ki=4.40,IC50=39.8uM
BindingDB: IC50=39800nM
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:3np9, PDBe:3np9, PDBj:3np9
PDBsum3np9
PubMed21821421
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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