Structure of PDB 3cut Chain A Binding Site BS01

Receptor Information
>3cut Chain A (length=813) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLNVGGYIQ
AVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSS
TNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCA
YTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVD
RLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYE
LEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLS
YVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEY
KRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLI
TAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEA
SGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQ
RGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKV
FADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYARE
IWGVEPSRQRLPA
Ligand information
Ligand ID179
InChIInChI=1S/C18H20N2O7/c21-8-12-13(22)14(23)15(24)18(27-12)20-17(26)16(25)19-11-6-5-9-3-1-2-4-10(9)7-11/h1-7,12-15,18,21-24H,8H2,(H,19,25)(H,20,26)/t12-,13-,14+,15-,18-/m1/s1
InChIKeyWDRIXCWRSIXUDT-VPKNTQAGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2cc(ccc2c1)NC(=O)C(=O)NC3C(C(C(C(O3)CO)O)O)O
OpenEye OEToolkits 1.5.0c1ccc2cc(ccc2c1)NC(=O)C(=O)N[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
CACTVS 3.341OC[CH]1O[CH](NC(=O)C(=O)Nc2ccc3ccccc3c2)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@@H](NC(=O)C(=O)Nc2ccc3ccccc3c2)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O=C(NC1OC(C(O)C(O)C1O)CO)C(=O)Nc3cc2ccccc2cc3
FormulaC18 H20 N2 O7
NameN-[(naphthalen-2-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine
ChEMBLCHEMBL1229682
DrugBank
ZINCZINC000039107492
PDB chain3cut Chain A Residue 998 [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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PDB3cut Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides
Resolution2.3 Å
Binding residue
(original residue number in PDB)		E88 G135 L136 N282 N284 F285 H341 H377 A383 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		E77 G124 L125 N268 N270 F271 H318 H354 A360 N461 E649 S651 G652
Annotation score1
Binding affinityBindingDB: Ki=56000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H354 K545 R546 K551 T653 K657
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:3cut, PDBe:3cut, PDBj:3cut
PDBsum3cut
PubMed
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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