Structure of PDB 1b4d Chain A Binding Site BS01

Receptor Information
>1b4d Chain A (length=804) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDH
LVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEAT
YQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYE
FGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQG
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNGYIQAVLDRNLA
ENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKNFDAFPD
KVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVIP
EALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLV
EEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQN
KTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFI
RDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCL
HVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVN
HDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKF
MLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEY
YDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYV
KCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSR
QRLP
Ligand information
Ligand IDCRA
InChIInChI=1S/C9H16N2O8/c1-18-8(17)11-9(7(10)16)6(15)5(14)4(13)3(2-12)19-9/h3-6,12-15H,2H2,1H3,(H2,10,16)(H,11,17)/t3-,4-,5+,6-,9+/m1/s1
InChIKeyZQTAMPRAONLFQI-FMTWGGRWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COC(=O)N[C@]1([C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O)C(=O)N
CACTVS 3.341COC(=O)N[C]1(O[CH](CO)[CH](O)[CH](O)[CH]1O)C(N)=O
OpenEye OEToolkits 1.5.0COC(=O)NC1(C(C(C(C(O1)CO)O)O)O)C(=O)N
CACTVS 3.341COC(=O)N[C@@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(N)=O
ACDLabs 10.04O=C(OC)NC1(OC(CO)C(O)C(O)C1O)C(=O)N
FormulaC9 H16 N2 O8
Name1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE
ChEMBLCHEMBL133097
DrugBankDB04013
ZINCZINC000004134471
PDB chain1b4d 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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PDB1b4d Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G135 L136 N284 H377 T378 N484 E672 S674 G675
Binding residue
(residue number reindexed from 1)		G123 L124 N262 H346 T347 N453 E641 S643 G644
Annotation score1
Binding affinityMOAD: Ki=15.6uM
PDBbind-CN: -logKd/Ki=4.81,Ki=15.6uM
BindingDB: Ki=16000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H346 K537 R538 K543 T645 K649
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:1b4d, PDBe:1b4d, PDBj:1b4d
PDBsum1b4d
PubMed10211820
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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