Structure of PDB 3ms2 Chain A Binding Site BS02

Receptor Information
>3ms2 Chain A (length=811) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGGYIQAV
LDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTN
FDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYT
NHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRL
RRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELE
PHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYV
DDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKR
QLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITA
IGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASG
TGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRG
YNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFA
DYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIW
GVEPSRQRLPA
Ligand information
Ligand ID18S
InChIInChI=1S/C15H21N3O5S/c1-8-2-4-9(5-3-8)6-16-18-15(24)17-14-13(22)12(21)11(20)10(7-19)23-14/h2-6,10-14,19-22H,7H2,1H3,(H2,17,18,24)/b16-6+/t10-,11-,12+,13-,14-/m1/s1
InChIKeyDVGNOMWZPXETCK-VSZQLFBDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1ccc(cc1)C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O
CACTVS 3.370Cc1ccc(cc1)\C=N\NC(=S)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
ACDLabs 12.01S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C/c2ccc(cc2)C
OpenEye OEToolkits 1.7.0Cc1ccc(cc1)/C=N/NC(=S)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.370Cc1ccc(cc1)C=NNC(=S)N[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O
FormulaC15 H21 N3 O5 S
NameN-({(2E)-2-[(4-methylphenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine;
4-methylbenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone
ChEMBL
DrugBank
ZINCZINC000058633555
PDB chain3ms2 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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PDB3ms2 The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E88 G135 L136 Y280 N282 D283 R292 H341 H377 V455 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		E77 G124 L125 Y264 N266 D267 R276 H316 H352 V430 N459 E647 S649 G650
Annotation score1
Binding affinityMOAD: ic50=192.4uM
PDBbind-CN: -logKd/Ki=3.72,IC50=192.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H352 K543 R544 K549 T651 K655
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
View graph for
Cellular Component
External links
PDB RCSB:3ms2, PDBe:3ms2, PDBj:3ms2
PDBsum3ms2
PubMed20947361
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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