Structure of PDB 6gg4 Chain A Binding Site BS01

Receptor Information
>6gg4 Chain A (length=509) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVA
RLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTG
LIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGS
KIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVS
EKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIE
NHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGK
PVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPL
EAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFK
CCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPV
LCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFT
NTMRVVPVP
Ligand information
Ligand IDPHE
InChIInChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1
InChIKeyCOLNVLDHVKWLRT-QMMMGPOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](Cc1ccccc1)C(O)=O
CACTVS 3.341N[C@@H](Cc1ccccc1)C(O)=O
OpenEye OEToolkits 1.5.0c1ccc(cc1)CC(C(=O)O)N
OpenEye OEToolkits 1.5.0c1ccc(cc1)C[C@@H](C(=O)O)N
ACDLabs 10.04O=C(O)C(N)Cc1ccccc1
FormulaC9 H11 N O2
NamePHENYLALANINE
ChEMBLCHEMBL301523
DrugBankDB00120
ZINCZINC000000105196
PDB chain6gg4 Chain A Residue 603 [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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PDB6gg4 An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor.
Resolution2.46 Å
Binding residue
(original residue number in PDB)		R43 N44 N70 H464 I469 F470
Binding residue
(residue number reindexed from 1)		R21 N22 N48 H442 I447 F448
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.69,Ki=205uM
Enzymatic activity
Catalytic site (original residue number in PDB) R73 R120 K270 T328
Catalytic site (residue number reindexed from 1) R51 R98 K248 T306
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6gg4, PDBe:6gg4, PDBj:6gg4
PDBsum6gg4
PubMed29748232
UniProtP14618|KPYM_HUMAN Pyruvate kinase PKM (Gene Name=PKM)

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