Structure of PDB 4lfi Chain B Binding Site BS01

Receptor Information
>4lfi Chain B (length=371) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKCRVWSEARVYTNINKQRTEEYWDYENTVIDWSTNTKDYEIENKVGRGK
YSEVFQGVKLDSKVKIVIKMLKPVKKKKIKREIKILTDLSNEKVPPTTLP
FQKDQYYTNQKEDVLKFIRPYIFDQPHNGHANIIHLFDIIKDPISKTPAL
VFEYVDNVDFRILYPKLTDLEIRFYMFELLKALDYCHSMGIMHRDVKPHN
VMIDHKNKKLRLIDWGLAEFYHVNMEYNVRVASRFFKGPELLVDYRMYDY
SLDLWSFGTMLASMIFKREPFFHGTSNTDQLVKIVKVLGTSDFEKYLLKY
EITLPREFYDMDQYIRKPWHRFINDGNKHLSGNDEIIDLIDNLLRYDHQE
RLTAKEAMGHPWFAPIREQIE
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain4lfi Chain B Residue 401 [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]
PDB4lfi The multiple nucleotide-divalent cation binding modes of Saccharomyces cerevisiae CK2 alpha indicate a possible co-substrate hydrolysis product (ADP/GDP) release pathway.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		G47 R48 G49 K50 Y51 S52 V54 V67 K69 V155 K197 H199 M202 I213 D214
Binding residue
(residue number reindexed from 1)		G47 R48 G49 K50 Y51 S52 V54 V67 K69 V155 K197 H199 M202 I213 D214
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) D195 K197 N200 D214 S233
Catalytic site (residue number reindexed from 1) D195 K197 N200 D214 S233
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0006338 chromatin remodeling
GO:0006356 regulation of transcription by RNA polymerase I
GO:0006359 regulation of transcription by RNA polymerase III
GO:0006468 protein phosphorylation
GO:0006974 DNA damage response
GO:0007535 donor selection
GO:0016310 phosphorylation
GO:0030490 maturation of SSU-rRNA
GO:0042790 nucleolar large rRNA transcription by RNA polymerase I
GO:0051726 regulation of cell cycle
GO:0060962 regulation of ribosomal protein gene transcription by RNA polymerase II
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0005956 protein kinase CK2 complex
GO:0032040 small-subunit processome
GO:0032545 CURI complex
GO:0034456 UTP-C complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4lfi, PDBe:4lfi, PDBj:4lfi
PDBsum4lfi
PubMed24531484
UniProtP15790|CSK21_YEAST Casein kinase II subunit alpha (Gene Name=CKA1)

[Back to BioLiP]