Structure of PDB 8f6m Chain F Binding Site BS01

Receptor Information
>8f6m Chain F (length=515) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVETLK
EMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVAL
DTKGPEIRTGLIKAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICK
VVDVGSKVYVDDGLISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAV
DLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKILGEKGKNIK
IISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMIIGR
CNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETA
KGDYPLEAVRMQHLIAREAEAAMFHRKLFEELARASSHSTDLMEAMAMGS
VEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLY
RGIFPVVCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTGWR
PGSGFTNTMRVVPVP
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8f6m Chain F Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8f6m PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		P52 R72 N74 H77 R119 G362 A365
Binding residue
(residue number reindexed from 1)		P41 R61 N63 H66 R108 G347 A350
Annotation score5
Enzymatic activity
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: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:0030955 potassium ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006096 glycolytic process
GO:0006417 regulation of translation
GO:0016310 phosphorylation
GO:0032869 cellular response to insulin stimulus
GO:1903672 positive regulation of sprouting angiogenesis
GO:2000767 positive regulation of cytoplasmic translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005791 rough endoplasmic reticulum

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8f6m, PDBe:8f6m, PDBj:8f6m
PDBsum8f6m
PubMed37171062
UniProtP11974|KPYM_RABIT Pyruvate kinase PKM (Gene Name=PKM)

[Back to BioLiP]