Structure of PDB 4mi6 Chain A Binding Site BS01

Receptor Information
>4mi6 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGGYIQAV
LDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA
Ligand information
Ligand ID26V
InChIInChI=1S/C20H29NO6/c22-11-15-17(24)18(25)19(26)20(27-15)21-16(23)7-3-4-12-8-9-13-5-1-2-6-14(13)10-12/h8-10,15,17-20,22,24-26H,1-7,11H2,(H,21,23)/t15-,17-,18+,19-,20-/m1/s1
InChIKeyXAFXSLABZKEYPA-XIKSMUEASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1CCCC(=O)N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)CCCC2
CACTVS 3.385OC[C@H]1O[C@@H](NC(=O)CCCc2ccc3CCCCc3c2)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.7.6c1cc2c(cc1CCCC(=O)NC3C(C(C(C(O3)CO)O)O)O)CCCC2
CACTVS 3.385OC[CH]1O[CH](NC(=O)CCCc2ccc3CCCCc3c2)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01O=C(NC1OC(C(O)C(O)C1O)CO)CCCc2ccc3c(c2)CCCC3
FormulaC20 H29 N O6
NameN-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine
ChEMBLCHEMBL3322333
DrugBank
ZINCZINC000098208100
PDB chain4mi6 Chain A Residue 901 [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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PDB4mi6 Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L136 D283 N284 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		L125 D267 N268 H351 N458 E646 S648 G649
Annotation score1
Binding affinityMOAD: Ki=48.68uM
PDBbind-CN: -logKd/Ki=4.31,Ki=48.68uM
BindingDB: Ki=48680nM
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:4mi6, PDBe:4mi6, PDBj:4mi6
PDBsum4mi6
PubMed25092521
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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