Structure of PDB 3nc4 Chain A Binding Site BS02

Receptor Information
>3nc4 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 ID26O
InChIInChI=1S/C14H19N3O6S/c18-6-9-10(20)11(21)12(22)13(23-9)16-14(24)17-15-5-7-3-1-2-4-8(7)19/h1-5,9-13,18-22H,6H2,(H2,16,17,24)/b15-5+/t9-,10-,11+,12-,13-/m1/s1
InChIKeyYXAUMHVOUHQJAX-IVSPNHRTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(c(c1)C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O)O
CACTVS 3.370OC[CH]1O[CH](NC(=S)NN=Cc2ccccc2O)[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1O[C@@H](NC(=S)N/N=C/c2ccccc2O)[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)O
ACDLabs 12.01S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C/c2ccccc2O
FormulaC14 H19 N3 O6 S
NameN-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine;
2-hydroxybenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone;
N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucosylamine;
N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-D-glucosylamine;
N-({(2E)-2-[(2-hydroxyphenyl)methylidene]hydrazino}carbonothioyl)-glucosylamine
ChEMBL
DrugBank
ZINCZINC000058632312
PDB chain3nc4 Chain A Residue 920 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nc4 The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
Resolution2.07 Å
Binding residue
(original residue number in PDB)		R60 V64 W67 E190 K191 A192 P229
Binding residue
(residue number reindexed from 1)		R49 V53 W56 E179 K180 A181 P218
Annotation score1
Binding affinityMOAD: ic50=26.6uM
PDBbind-CN: -logKd/Ki=4.58,IC50=26.6uM
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:3nc4, PDBe:3nc4, PDBj:3nc4
PDBsum3nc4
PubMed20947361
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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