Structure of PDB 3ms7 Chain A Binding Site BS02

Receptor Information
>3ms7 Chain A (length=809) 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
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNFD
AFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNH
TVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRR
MSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPH
KFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDD
EAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQL
LNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIG
DVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTG
NMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYN
AQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADY
EEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGV
EPSRQRLPA
Ligand information
Ligand ID22S
InChIInChI=1S/C14H18ClN3O5S/c15-8-4-2-1-3-7(8)5-16-18-14(24)17-13-12(22)11(21)10(20)9(6-19)23-13/h1-5,9-13,19-22H,6H2,(H2,17,18,24)/b16-5+/t9-,10-,11+,12-,13-/m1/s1
InChIKeyHKDGHOCNKASZRS-QCOQDYPWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(c(c1)C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O)Cl
CACTVS 3.370OC[C@H]1O[C@@H](NC(=S)N\N=C\c2ccccc2Cl)[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)Cl
ACDLabs 12.01S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C/c2ccccc2Cl
CACTVS 3.370OC[CH]1O[CH](NC(=S)NN=Cc2ccccc2Cl)[CH](O)[CH](O)[CH]1O
FormulaC14 H18 Cl N3 O5 S
NameN-({(2E)-2-[(2-chlorophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucopyranosylamine;
2-chlorobenzaldehyde-4-(beta-D-glucopyranosyl) thiosemicarbazone;
N-({(2E)-2-[(2-chlorophenyl)methylidene]hydrazino}carbonothioyl)-beta-D-glucosylamine;
N-({(2E)-2-[(2-chlorophenyl)methylidene]hydrazino}carbonothioyl)-D-glucosylamine;
N-({(2E)-2-[(2-chlorophenyl)methylidene]hydrazino}carbonothioyl)-glucosylamine
ChEMBL
DrugBank
ZINCZINC000058631759
PDB chain3ms7 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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PDB3ms7 The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		E88 G135 L136 N282 D283 N284 F285 H341 H377 A383 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		E77 G124 L125 N265 D266 N267 F268 H314 H350 A356 N457 E645 S647 G648
Annotation score1
Binding affinityMOAD: ic50=370uM
PDBbind-CN: -logKd/Ki=3.43,IC50=370uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H350 K541 R542 K547 T649 K653
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:3ms7, PDBe:3ms7, PDBj:3ms7
PDBsum3ms7
PubMed20947361
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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