Structure of PDB 4mic Chain A Binding Site BS01

Receptor Information
>4mic 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 ID26Y
InChIInChI=1S/C18H25NO6/c1-10(2)12-6-3-11(4-7-12)5-8-14(21)19-18-17(24)16(23)15(22)13(9-20)25-18/h3-8,10,13,15-18,20,22-24H,9H2,1-2H3,(H,19,21)/b8-5+/t13-,15-,16+,17-,18-/m1/s1
InChIKeyOPYZIUIJGFRFFX-AWRGUQPNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)c1ccc(C=CC(=O)N[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)cc1
CACTVS 3.385CC(C)c1ccc(/C=C/C(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)cc1
OpenEye OEToolkits 1.7.6CC(C)c1ccc(cc1)/C=C/C(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
OpenEye OEToolkits 1.7.6CC(C)c1ccc(cc1)C=CC(=O)NC2C(C(C(C(O2)CO)O)O)O
ACDLabs 12.01O=C(NC1OC(C(O)C(O)C1O)CO)\C=C\c2ccc(cc2)C(C)C
FormulaC18 H25 N O6
NameN-{(2E)-3-[4-(propan-2-yl)phenyl]prop-2-enoyl}-beta-D-glucopyranosylamine
ChEMBLCHEMBL3322337
DrugBank
ZINCZINC000098208102
PDB chain4mic 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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PDB4mic Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		G135 L136 N282 D283 F285 H341 H377 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G124 L125 N262 D263 F265 H312 H348 N455 E643 S645 G646
Annotation score1
Binding affinityMOAD: Ki=4.98uM
PDBbind-CN: -logKd/Ki=5.30,Ki=4.98uM
BindingDB: Ki=4980nM
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
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Biological Process
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Cellular Component
External links
PDB RCSB:4mic, PDBe:4mic, PDBj:4mic
PDBsum4mic
PubMed25092521
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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