Structure of PDB 4rpp Chain C Binding Site BS01

Receptor Information

>4rpp Chain C (length=396) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVAR
LNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPAVSEKD
IQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHE
GVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVI
CATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAV
RMQHLIAREAEAAIYHLQLFEELRRLITSDPTEATAVGAVEASFRCCSGA
IIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDP
VQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGNTMRVVPVP

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

4rpp Chain C Residue 600 [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	4rpp Structural insight into mechanisms for dynamic regulation of PKM2.
Resolution	2.585 Å
Binding residue (original residue number in PDB)	L431 T432 K433 S434 S437 R489 G514
Binding residue (residue number reindexed from 1)	L304 T305 K306 S307 S310 R362 G387
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	R73 K270 T328
Catalytic site (residue number reindexed from 1)	R50 K145 T203
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:4rpp, PDBe:4rpp, PDBj:4rpp
PDBsum	4rpp
PubMed	25645022
UniProt	P14618\|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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