Structure of PDB 4mi3 Chain A Binding Site BS01

Receptor Information
>4mi3 Chain A (length=807) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDGYIQAVLDRN
LAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNFDAF
PDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTV
LPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMS
LVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKF
QNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEA
FIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLN
CLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDV
VNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNM
KFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQ
EYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEE
YVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEP
SRQRLPA
Ligand information
Ligand ID26R
InChIInChI=1S/C19H29NO6/c1-10(2)13-6-4-12(5-7-13)8-11(3)18(25)20-19-17(24)16(23)15(22)14(9-21)26-19/h4-7,10-11,14-17,19,21-24H,8-9H2,1-3H3,(H,20,25)/t11-,14-,15-,16+,17-,19-/m1/s1
InChIKeyHJOFLVJJICDECE-YMZRVSMESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)c1ccc(cc1)CC(C)C(=O)NC2C(C(C(C(O2)CO)O)O)O
OpenEye OEToolkits 1.7.6C[C@H](Cc1ccc(cc1)C(C)C)C(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.385CC(C)c1ccc(C[C@@H](C)C(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)cc1
ACDLabs 12.01O=C(NC1OC(C(O)C(O)C1O)CO)C(C)Cc2ccc(cc2)C(C)C
CACTVS 3.385CC(C)c1ccc(C[CH](C)C(=O)N[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)cc1
FormulaC19 H29 N O6
NameN-{(2R)-2-methyl-3-[4-(propan-2-yl)phenyl]propanoyl}-beta-D-glucopyranosylamine
ChEMBL
DrugBank
ZINCZINC000098208099
PDB chain4mi3 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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PDB4mi3 Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G135 L136 D283 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 D263 H348 N455 E643 S645 G646
Annotation score1
Binding affinityMOAD: Ki=75.29uM
PDBbind-CN: -logKd/Ki=4.12,Ki=75.29uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H348 K539 R540 K545 T647 K651
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
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:4mi3, PDBe:4mi3, PDBj:4mi3
PDBsum4mi3
PubMed25092521
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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