Structure of PDB 3msc Chain A Binding Site BS02

Receptor Information
>3msc 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 ID24S
InChIInChI=1S/C14H18N4O7S/c19-6-9-10(20)11(21)12(22)13(25-9)16-14(26)17-15-5-7-3-1-2-4-8(7)18(23)24/h1-5,9-13,19-22H,6H2,(H2,16,17,26)/b15-5-/t9-,10-,11+,12-,13-/m1/s1
InChIKeyHIBBBAGNJNCOKR-ARDSGTFASA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[C@H]1O[C@@H](NC(=S)N\N=C/c2ccccc2[N+]([O-])=O)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.7.0c1ccc(c(c1)/C=N\NC(=S)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)[N+](=O)[O-]
ACDLabs 12.01S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C\c2ccccc2[N+]([O-])=O
OpenEye OEToolkits 1.7.0c1ccc(c(c1)C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O)[N+](=O)[O-]
CACTVS 3.370OC[CH]1O[CH](NC(=S)NN=Cc2ccccc2[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
FormulaC14 H18 N4 O7 S
NameN-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine;
2-nitrobenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone;
N-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucosylamine;
N-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-D-glucosylamine;
N-({(2Z)-2-[(2-nitrophenyl)methylidene]hydrazino}carbonothioyl)-glucosylamine
ChEMBL
DrugBank
ZINCZINC000064426515
PDB chain3msc Chain A Residue 844 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3msc The binding of beta-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors.
Resolution1.951 Å
Binding residue
(original residue number in PDB)		R60 W189 E190 K191 P229
Binding residue
(residue number reindexed from 1)		R49 W178 E179 K180 P218
Annotation score1
Binding affinityMOAD: ic50=484.2uM
PDBbind-CN: -logKd/Ki=3.31,IC50=484.2uM
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:3msc, PDBe:3msc, PDBj:3msc
PDBsum3msc
PubMed20947361
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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