Structure of PDB 2gm9 Chain A Binding Site BS02

Receptor Information
>2gm9 Chain A (length=805) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNGGYIQAVLDRN
LAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSNFDAFPD
KVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLP
EALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLV
EEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQN
KTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFI
RDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCL
HVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVN
HDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKF
MLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEY
YDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYV
KCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSR
QRLPA
Ligand information
Ligand ID3TH
InChIInChI=1S/C16H12ClN3O2S/c17-13-7-9-6-12(20-16(9)23-13)15(22)19-11-5-8-3-1-2-4-10(8)18-14(11)21/h1-4,6-7,11,20H,5H2,(H,18,21)(H,19,22)/t11-/m1/s1
InChIKeyLJAHIGGEXIWVJG-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc2c(c1)CC(C(=O)N2)NC(=O)c3cc4cc(sc4[nH]3)Cl
OpenEye OEToolkits 1.5.0c1ccc2c(c1)C[C@H](C(=O)N2)NC(=O)c3cc4cc(sc4[nH]3)Cl
CACTVS 3.341Clc1sc2[nH]c(cc2c1)C(=O)N[C@@H]3Cc4ccccc4NC3=O
CACTVS 3.341Clc1sc2[nH]c(cc2c1)C(=O)N[CH]3Cc4ccccc4NC3=O
ACDLabs 10.04Clc2sc1nc(cc1c2)C(=O)NC4C(=O)Nc3ccccc3C4
FormulaC16 H12 Cl N3 O2 S
Name2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
ChEMBL
DrugBankDB07066
ZINCZINC000034855090
PDB chain2gm9 Chain A Residue 1 [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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PDB2gm9 Novel thienopyrrole glycogen phosphorylase inhibitors: synthesis, in vitro SAR and crystallographic studies.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R60 W67 W189 E190 K191
Binding residue
(residue number reindexed from 1)		R49 W56 W178 E179 K180
Annotation score1
Binding affinityMOAD: ic50=41nM
PDBbind-CN: -logKd/Ki=7.39,IC50=41nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2gm9, PDBe:2gm9, PDBj:2gm9
PDBsum2gm9
PubMed16945526
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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