Structure of PDB 6gzd Chain A Binding Site BS02

Receptor Information
>6gzd Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFIVGGKYKLGRKIGSGSFGDIYLATNITNGEEVAVKLESQKARHPQLH
YESKLYKILQGGVGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRF
TMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDF
GLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLG
YVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAM
YLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKA
Ligand information
Ligand IDLCI
InChIInChI=1S/C18H25FN6/c1-25-16(8-11-2-3-11)14(9-22-25)17-15(19)10-21-18(24-17)23-13-6-4-12(20)5-7-13/h9-13H,2-8,20H2,1H3,(H,21,23,24)/p+1/t12-,13-
InChIKeyYSPIHUWHLMNFOV-JOCQHMNTSA-O
SMILES
SoftwareSMILES
CACTVS 3.385Cn1ncc(c1CC2CC2)c3nc(N[C@H]4CC[C@H]([NH3+])CC4)ncc3F
CACTVS 3.385Cn1ncc(c1CC2CC2)c3nc(N[CH]4CC[CH]([NH3+])CC4)ncc3F
OpenEye OEToolkits 2.0.6Cn1c(c(cn1)c2c(cnc(n2)NC3CCC(CC3)[NH3+])F)CC4CC4
FormulaC18 H26 F N6
Name[4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium
ChEMBL
DrugBank
ZINC
PDB chain6gzd Chain A Residue 1018 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6gzd Small Molecules Co-targeting CKI alpha and the Transcriptional Kinases CDK7/9 Control AML in Preclinical Models.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		S25 I31 A44 M90 L93 D99 L143
Binding residue
(residue number reindexed from 1)		S17 I23 A36 M82 L85 D91 L135
Annotation score1
Binding affinityMOAD: Kd=9.8nM
PDBbind-CN: -logKd/Ki=8.01,Kd=9.8nM
Enzymatic activity
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:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0007030 Golgi organization
GO:0007165 signal transduction
GO:0007166 cell surface receptor signaling pathway
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0019082 viral protein processing
GO:0031670 cellular response to nutrient
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0035025 positive regulation of Rho protein signal transduction
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045104 intermediate filament cytoskeleton organization
GO:0051301 cell division
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:1900226 negative regulation of NLRP3 inflammasome complex assembly
GO:1904263 positive regulation of TORC1 signaling
Cellular Component
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0030877 beta-catenin destruction complex
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:0045095 keratin filament

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6gzd, PDBe:6gzd, PDBj:6gzd
PDBsum6gzd
PubMed30146162
UniProtP48729|KC1A_HUMAN Casein kinase I isoform alpha (Gene Name=CSNK1A1)

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