Structure of PDB 3ms4 Chain A Binding Site BS02

Receptor Information
>3ms4 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 ID21N
InChIInChI=1S/C15H18F3N3O5S/c16-15(17,18)8-3-1-7(2-4-8)5-19-21-14(27)20-13-12(25)11(24)10(23)9(6-22)26-13/h1-5,9-13,22-25H,6H2,(H2,20,21,27)/b19-5+/t9-,10-,11+,12-,13-/m1/s1
InChIKeySPEHXGJLVCNQJH-HORNZCGOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(ccc1C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O)C(F)(F)F
OpenEye OEToolkits 1.7.0c1cc(ccc1/C=N/NC(=S)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)C(F)(F)F
ACDLabs 12.01S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C/c2ccc(cc2)C(F)(F)F
CACTVS 3.370OC[CH]1O[CH](NC(=S)NN=Cc2ccc(cc2)C(F)(F)F)[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1O[C@@H](NC(=S)N/N=C/c2ccc(cc2)C(F)(F)F)[C@H](O)[C@@H](O)[C@@H]1O
FormulaC15 H18 F3 N3 O5 S
NameN-{[(2E)-2-{[4-(trifluoromethyl)phenyl]methylidene}hydrazino]carbonothioyl}-beta-D-glucopyranosylamine;
4-trifluoromethylbenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone
ChEMBL
DrugBank
ZINCZINC000058631513
PDB chain3ms4 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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PDB3ms4 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)		E88 G135 L136 Y280 N282 R292 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		E77 G124 L125 Y263 N265 R275 H351 N458 E646 A647 S648 G649
Annotation score1
Binding affinityMOAD: ic50=524.3uM
PDBbind-CN: -logKd/Ki=3.28,IC50=524.3uM
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:3ms4, PDBe:3ms4, PDBj:3ms4
PDBsum3ms4
PubMed20947361
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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