Structure of PDB 4yi3 Chain A Binding Site BS02

Receptor Information
>4yi3 Chain A (length=806) 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
LAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSNFDAFP
DKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVL
PEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSL
VEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQ
NKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAF
IRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNC
LHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVV
NHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMK
FMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQE
YYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEY
VKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPS
RQRLPA
Ligand information
Ligand ID4D0
InChIInChI=1S/C22H26N2O7/c25-12-16-18(27)19(28)20(29)21(31-16)24-22(30)23-17(26)11-8-13-6-9-15(10-7-13)14-4-2-1-3-5-14/h1-7,9-10,16,18-21,25,27-29H,8,11-12H2,(H2,23,24,26,30)/t16-,18-,19+,20-,21-/m1/s1
InChIKeyDTCZORBBXRCGBE-QNDFHXLGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)c2ccc(cc2)CCC(=O)NC(=O)N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
OpenEye OEToolkits 1.9.2c1ccc(cc1)c2ccc(cc2)CCC(=O)NC(=O)NC3C(C(C(C(O3)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH](NC(=O)NC(=O)CCc2ccc(cc2)c3ccccc3)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H]1O[C@@H](NC(=O)NC(=O)CCc2ccc(cc2)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 12.01c1c(ccc(c1)CCC(=O)NC(=O)NC2OC(CO)C(O)C(C2O)O)c3ccccc3
FormulaC22 H26 N2 O7
NameN-{[3-(biphenyl-4-yl)propanoyl]carbamoyl}-beta-D-glucopyranosylamine
ChEMBL
DrugBank
ZINCZINC000263620374
PDB chain4yi3 Chain A Residue 902 [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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PDB4yi3 Glycogen phosphorylase as a target for type 2 diabetes: synthetic, biochemical, structural and computational evaluation of novel N-acyl-N -( beta-D-glucopyranosyl) urea inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N133 G135 L136 N282 D283 F286 R292 H341 H377 N484 E672 A673 S674 G675
Binding residue
(residue number reindexed from 1)		N122 G124 L125 N262 D263 F266 R272 H311 H347 N454 E642 A643 S644 G645
Annotation score1
Binding affinityMOAD: Ki=4.95uM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H347 K538 R539 K544 T646 K650
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:4yi3, PDBe:4yi3, PDBj:4yi3
PDBsum4yi3
PubMed26088352
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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