Structure of PDB 3me3 Chain B Binding Site BS02

Receptor Information

>3me3 Chain B (length=498) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKE
MIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALD
TKGPEIRTGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDD
GLISLQVDFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGV
EQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEI
LEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLES
MIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAR
EAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTK
SGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWA
EDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Ligand information

Ligand ID

FBP

InChI

InChI=1S/C6H14O12P2/c7-4-3(1-16-19(10,11)12)18-6(9,5(4)8)2-17-20(13,14)15/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4-,5+,6-/m1/s1

InChIKey

RNBGYGVWRKECFJ-ARQDHWQXSA-N

SMILES

Software	SMILES
CACTVS 3.341	O[C@H]1[C@H](O)[C@@](O)(CO[P](O)(O)=O)O[C@@H]1CO[P](O)(O)=O
CACTVS 3.341	O[CH]1[CH](O)[C](O)(CO[P](O)(O)=O)O[CH]1CO[P](O)(O)=O
ACDLabs 10.04	O=P(O)(O)OCC1OC(O)(COP(=O)(O)O)C(O)C1O
OpenEye OEToolkits 1.5.0	C(C1C(C(C(O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0	C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O

Formula

C6 H14 O12 P2

Name

1,6-di-O-phosphono-beta-D-fructofuranose;
BETA-FRUCTOSE-1,6-DIPHOSPHATE;
FRUCTOSE-1,6-BISPHOSPHATE;
1,6-di-O-phosphono-beta-D-fructose;
1,6-di-O-phosphono-D-fructose;
1,6-di-O-phosphono-fructose

PDB chain

3me3 Chain B Residue 541 [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	3me3 Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis.
Resolution	1.95 Å
Binding residue (original residue number in PDB)	L431 T432 K433 S434 S437 W482 R489 G514 R516 P517 G518 S519 G520 F521 T522
Binding residue (residue number reindexed from 1)	L398 T399 K400 S401 S404 W449 R456 G481 R483 P484 G485 S486 G487 F488 T489
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	R73 R120 K270 T328
Catalytic site (residue number reindexed from 1)	R60 R107 K237 T295
Enzyme Commision number	2.7.10.2: non-specific protein-tyrosine kinase. 2.7.11.1: non-specific serine/threonine protein kinase. 2.7.1.40: pyruvate kinase.

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0003723	RNA binding
GO:0003729	mRNA binding
GO:0003824	catalytic activity
GO:0004713	protein tyrosine kinase activity
GO:0004743	pyruvate kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0016301	kinase activity
GO:0023026	MHC class II protein complex binding
GO:0030955	potassium ion binding
GO:0045296	cadherin binding
GO:0046872	metal ion binding

	Biological Process
GO:0006096	glycolytic process
GO:0006417	regulation of translation
GO:0012501	programmed cell death
GO:0016310	phosphorylation
GO:0032869	cellular response to insulin stimulus
GO:0061621	canonical glycolysis
GO:1903672	positive regulation of sprouting angiogenesis
GO:2000767	positive regulation of cytoplasmic translation

	Cellular Component
GO:0005576	extracellular region
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005791	rough endoplasmic reticulum
GO:0005829	cytosol
GO:0005929	cilium
GO:0031982	vesicle
GO:0034774	secretory granule lumen
GO:0062023	collagen-containing extracellular matrix
GO:0070062	extracellular exosome
GO:1903561	extracellular vesicle
GO:1904813	ficolin-1-rich granule lumen

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Cellular Component

External links

PDB	RCSB:3me3, PDBe:3me3, PDBj:3me3
PDBsum	3me3
PubMed	22922757
UniProt	P14618\|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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