Structure of PDB 2ds1 Chain A Binding Site BS01

Receptor Information
>2ds1 Chain A (length=290) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIVPSTAIREISLLKEL
NHPNIVKLLDVIHTENKLYLVFEHVHQDLKTFMDASALTGIPLPLIKSYL
FQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRT
YTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSE
IDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDED
GRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Ligand information
Ligand ID1CD
InChIInChI=1S/C22H21N5O3/c1-12-10-13-11-26(12)8-9-27-22(29)15-5-2-4-14(18(15)25-27)19-21(28)23-16-6-3-7-17(30-13)20(16)24-19/h2-7,12-13,25H,8-11H2,1H3,(H,23,28)/t12-,13+/m1/s1
InChIKeyKBLPHMRCKHFBJB-OLZOCXBDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@H]1C[C@H]2C[N@]1CCN3C(=O)c4cccc(c4N3)C5=Nc6c(cccc6O2)NC5=O
ACDLabs 10.04O=C5Nc3cccc4OC6CN(CCN2Nc1c(cccc1C2=O)C5=Nc34)C(C)C6
OpenEye OEToolkits 1.5.0CC1CC2CN1CCN3C(=O)c4cccc(c4N3)C5=Nc6c(cccc6O2)NC5=O
CACTVS 3.341C[C@@H]1C[C@H]2CN1CCN3Nc4c(cccc4C5=Nc6c(NC5=O)cccc6O2)C3=O
CACTVS 3.341C[CH]1C[CH]2CN1CCN3Nc4c(cccc4C5=Nc6c(NC5=O)cccc6O2)C3=O
FormulaC22 H21 N5 O3
Name(13R,15S)-13-METHYL-16-OXA-8,9,12,22,24-PENTAAZAHEXACYCLO[15.6.2.16,9.1,12,15.0,2,7.0,21,25]HEPTACOSA-1(24),2,4,6,17(25 ),18,20-HEPTAENE-23,26-DIONE;
5H,10H-17,19-(IMINOMETHANO)-4,6:9,12-DIMETHANODIBENZ[B,F][1,4,8,9,12]OXATETRAAZACYCLOPENTADECINE-20,23-DIONE,7,8,11,12- TETRAHYDRO-10-METHYL-,(10R,12S)
ChEMBL
DrugBankDB06888
ZINCZINC000003820290
PDB chain2ds1 Chain A Residue 501 [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]
PDB2ds1 Structure-based drug design of a highly potent CDK1,2,4,6 inhibitor with novel macrocyclic quinoxalin-2-one structure
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I10 G13 V18 A31 K33 V64 F80 H82 V83 Q131 L134 D145
Binding residue
(residue number reindexed from 1)		I10 G13 V18 A31 K33 V56 F72 H74 V75 Q123 L126 D137
Annotation score1
Binding affinityMOAD: ic50=3.4nM
PDBbind-CN: -logKd/Ki=8.47,IC50=3.4nM
BindingDB: IC50=3.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D127 K129 Q131 N132 D145 T158 T165
Catalytic site (residue number reindexed from 1) D119 K121 Q123 N124 D137 T150 T157
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
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:2ds1, PDBe:2ds1, PDBj:2ds1
PDBsum2ds1
PubMed16876403
UniProtP24941|CDK2_HUMAN Cyclin-dependent kinase 2 (Gene Name=CDK2)

[Back to BioLiP]