Structure of PDB 3msc Chain A Binding Site BS01

Receptor Information

>3msc Chain A (length=810) Species: 9986 (Oryctolagus cuniculus)

QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRD
HLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEA
TYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQ
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA

Ligand information

• Ligand ID: 24S
• InChI: InChI=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
• InChIKey: HIBBBAGNJNCOKR-ARDSGTFASA-N
• SMILES:
  CACTVS 3.370: OC[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 1.7.0: c1ccc(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 12.01: S=C(NC1OC(C(O)C(O)C1O)CO)N/N=C\c2ccccc2[N+]([O-])=O
  OpenEye OEToolkits 1.7.0: c1ccc(c(c1)C=NNC(=S)NC2C(C(C(C(O2)CO)O)O)O)[N+](=O)[O-]
  CACTVS 3.370: OC[CH]1O[CH](NC(=S)NN=Cc2ccccc2[N+]([O-])=O)[CH](O)[CH](O)[CH]1O
• Formula: C14 H18 N4 O7 S
• Name: N-({(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
• ZINC: ZINC000064426515
• PDB chain: 3msc Chain A Residue 843

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3msc The binding of beta-d-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: A new class of inhibitors.
• Resolution: 1.951 Å
• Binding residue (original residue number in PDB): E88 N133 G135 L136 N282 D283 N284 F285 H341 H377 N484 E672 S674 G675
• Binding residue (residue number reindexed from 1): E77 N122 G124 L125 N265 D266 N267 F268 H315 H351 N458 E646 S648 G649
• Annotation score: 1
• Binding affinity: MOAD: 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

External links

• PDB: RCSB:3msc, PDBe:3msc, PDBj:3msc
• PDBsum: 3msc
• PubMed: 20947361
• UniProt: P00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)