Structure of PDB 4tth Chain B Binding Site BS01

Receptor Information
>4tth Chain B (length=256) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CVAEIGEKVFKARDLKNGRFVALKRVRVEGMPLSTIREVAVLRHLETFEH
PNVVRLFDVCTTKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLL
RGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVV
VTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGK
ILDVIGLPGEEDWPPIEKFDIDELGKDLLLKCLTFNPAKRISAYSALSHP
YFQDLE
Ligand information
Ligand ID24V
InChIInChI=1S/C23H26N8/c1-2-4-16(3-1)31-20-15-25-8-7-18(20)19-14-27-23(29-22(19)31)28-21-6-5-17(13-26-21)30-11-9-24-10-12-30/h5-8,13-16,24H,1-4,9-12H2,(H,26,27,28,29)
InChIKeyMCPPMOSBWNMSOA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C1CCC(C1)n2c3cnccc3c4cnc(Nc5ccc(cn5)N6CCNCC6)nc24
ACDLabs 12.01n1cc(ccc1Nc4nc3n(c2c(ccnc2)c3cn4)C5CCCC5)N6CCNCC6
OpenEye OEToolkits 1.9.2c1cc(ncc1N2CCNCC2)Nc3ncc4c5ccncc5n(c4n3)C6CCCC6
FormulaC23 H26 N8
Name9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine
ChEMBLCHEMBL3237442
DrugBank
ZINCZINC000087493449
PDB chain4tth 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

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PDB4tth Discovery of AMG 925, a FLT3 and CDK4 dual kinase inhibitor with preferential affinity for the activated state of FLT3.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		I19 V27 A41 F98 V101 D102 D104 T107 Q149 L152
Binding residue
(residue number reindexed from 1)		I5 V9 A22 F68 V71 D72 D74 T77 Q119 L122
Annotation score1
Binding affinityBindingDB: IC50=4.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D145 K147 Q149 N150 D163 A175 T182
Catalytic site (residue number reindexed from 1) D115 K117 Q119 N120 D133 A145 T152
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
Gene Ontology
Molecular Function
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:0030332 cyclin binding
GO:0098770 FBXO family protein binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002244 hematopoietic progenitor cell differentiation
GO:0003323 type B pancreatic cell development
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0007219 Notch signaling pathway
GO:0008285 negative regulation of cell population proliferation
GO:0009615 response to virus
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010468 regulation of gene expression
GO:0010628 positive regulation of gene expression
GO:0014002 astrocyte development
GO:0016310 phosphorylation
GO:0021542 dentate gyrus development
GO:0021670 lateral ventricle development
GO:0030097 hemopoiesis
GO:0030154 cell differentiation
GO:0033077 T cell differentiation in thymus
GO:0042063 gliogenesis
GO:0042127 regulation of cell population proliferation
GO:0043697 cell dedifferentiation
GO:0045596 negative regulation of cell differentiation
GO:0045638 negative regulation of myeloid cell differentiation
GO:0045646 regulation of erythrocyte differentiation
GO:0045656 negative regulation of monocyte differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045786 negative regulation of cell cycle
GO:0048146 positive regulation of fibroblast proliferation
GO:0048699 generation of neurons
GO:0050680 negative regulation of epithelial cell proliferation
GO:0051301 cell division
GO:0051726 regulation of cell cycle
GO:0060218 hematopoietic stem cell differentiation
GO:1902036 regulation of hematopoietic stem cell differentiation
GO:2000145 regulation of cell motility
GO:2000773 negative regulation of cellular senescence
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0001726 ruffle
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0042995 cell projection
GO:0097131 cyclin D1-CDK6 complex
GO:0097132 cyclin D2-CDK6 complex
GO:0097133 cyclin D3-CDK6 complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4tth, PDBe:4tth, PDBj:4tth
PDBsum4tth
PubMed24641103
UniProtQ00534|CDK6_HUMAN Cyclin-dependent kinase 6 (Gene Name=CDK6)

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