Structure of PDB 3ns9 Chain A

Receptor sequence

>3ns9A (length=289) Species: 9606 (Homo sapiens) [Search protein sequence]

NFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIGVPSTAIREISLLKELN
HPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLF
QLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTY
THEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEI
DQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDG
RSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

3D structure

PDB

3ns9 A Novel Pyrazolo[1,5-a]pyrimidine Is a Potent Inhibitor of Cyclin-Dependent Protein Kinases 1, 2, and 9, Which Demonstrates Antitumor Effects in Human Tumor Xenografts Following Oral Administration.

Chain

Resolution

1.78 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	D127 K129 Q131 N132 D145 T158 T165
Catalytic site (residue number reindexed from 1)	D118 K120 Q122 N123 D136 T149 T156
Enzyme Commision number	2.7.11.22: cyclin-dependent kinase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	NS9	A	I10 V18 A31 F80 F82 L83 Q85 L134	I8 V16 A29 F71 F73 L74 Q76 L125	MOAD: ic50=0.003uM PDBbind-CN: -logKd/Ki=8.52,IC50=3nM BindingDB: IC50=3nM

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0004672	protein kinase activity
GO:0004674	protein serine/threonine kinase activity
GO:0004693	cyclin-dependent protein serine/threonine kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0016301	kinase activity
GO:0019904	protein domain specific binding
GO:0030332	cyclin binding
GO:0035173	histone kinase activity
GO:0046872	metal ion binding
GO:0097472	cyclin-dependent protein kinase activity
GO:0106310	protein serine kinase activity

	Biological Process
GO:0000082	G1/S transition of mitotic cell cycle
GO:0000086	G2/M transition of mitotic cell cycle
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0006260	DNA replication
GO:0006281	DNA repair
GO:0006338	chromatin remodeling
GO:0006351	DNA-templated transcription
GO:0006468	protein phosphorylation
GO:0006813	potassium ion transport
GO:0007099	centriole replication
GO:0007165	signal transduction
GO:0007265	Ras protein signal transduction
GO:0007346	regulation of mitotic cell cycle
GO:0008284	positive regulation of cell population proliferation
GO:0010389	regulation of G2/M transition of mitotic cell cycle
GO:0010468	regulation of gene expression
GO:0016310	phosphorylation
GO:0018105	peptidyl-serine phosphorylation
GO:0031453	positive regulation of heterochromatin formation
GO:0031571	mitotic G1 DNA damage checkpoint signaling
GO:0032298	positive regulation of DNA-templated DNA replication initiation
GO:0043247	telomere maintenance in response to DNA damage
GO:0043687	post-translational protein modification
GO:0045740	positive regulation of DNA replication
GO:0045893	positive regulation of DNA-templated transcription
GO:0051298	centrosome duplication
GO:0051301	cell division
GO:0051321	meiotic cell cycle
GO:0071732	cellular response to nitric oxide
GO:0090398	cellular senescence
GO:1905784	regulation of anaphase-promoting complex-dependent catabolic process

	Cellular Component
GO:0000307	cyclin-dependent protein kinase holoenzyme complex
GO:0000781	chromosome, telomeric region
GO:0000793	condensed chromosome
GO:0000805	X chromosome
GO:0000806	Y chromosome
GO:0001673	male germ cell nucleus
GO:0005634	nucleus
GO:0005635	nuclear envelope
GO:0005654	nucleoplasm
GO:0005667	transcription regulator complex
GO:0005737	cytoplasm
GO:0005768	endosome
GO:0005813	centrosome
GO:0005829	cytosol
GO:0005856	cytoskeleton
GO:0015030	Cajal body
GO:0097123	cyclin A1-CDK2 complex
GO:0097124	cyclin A2-CDK2 complex
GO:0097134	cyclin E1-CDK2 complex
GO:0097135	cyclin E2-CDK2 complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3ns9, PDBe:3ns9, PDBj:3ns9
PDBsum	3ns9
PubMed	21080703
UniProt	P24941\|CDK2_HUMAN Cyclin-dependent kinase 2 (Gene Name=CDK2)

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