Structure of PDB 6s4k Chain A Binding Site BS01

Receptor Information

>6s4k Chain A (length=810) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSTNF
DAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTN
HTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLR
RMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEP
HKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVD
DEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQ
LLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAI
GDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGT
GNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGY
NAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFAD
YEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWG
VEPSRQRLPA

Ligand information

Ligand ID

KVW

InChI

InChI=1S/C15H17NO5S/c17-6-10-11(18)12(19)13(20)14(21-10)15-16-9(7-22-15)8-4-2-1-3-5-8/h1-5,7,10-14,17-20H,6H2/t10-,11-,12+,13-,14-/m1/s1

InChIKey

CQDQZIAPWGJSQJ-RKQHYHRCSA-N

SMILES

Software	SMILES
CACTVS 3.385	OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2scc(n2)c3ccccc3
OpenEye OEToolkits 2.0.7	c1ccc(cc1)c2csc(n2)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
OpenEye OEToolkits 2.0.7	c1ccc(cc1)c2csc(n2)C3C(C(C(C(O3)CO)O)O)O
CACTVS 3.385	OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2scc(n2)c3ccccc3

Formula

C15 H17 N O5 S

Name

(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-phenyl-1,3-thiazol-2-yl)oxane-3,4,5-triol

PDB chain

6s4k Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6s4k The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design.
Resolution	2.43 Å
Binding residue (original residue number in PDB)	G135 L136 N282 N284 H341 H377 N484 E672 S674 G675
Binding residue (residue number reindexed from 1)	G124 L125 N265 N267 H315 H351 N458 E646 S648 G649
Annotation score	1
Binding affinity	MOAD: Ki=310uM BindingDB: Ki=310000nM

Enzymatic activity

Catalytic site (original residue number in PDB)	H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1)	H351 K542 R543 K548 T650 K654
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:6s4k, PDBe:6s4k, PDBj:6s4k
PDBsum	6s4k
PubMed	31767404
UniProt	P00489\|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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