Structure of PDB 2j2i Chain B Binding Site BS01

Receptor Information
>2j2i Chain B (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPN
GTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDF
ITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGEL
KLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILL
YDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFE
EIQNHPWMQDVLLPQETAEIHLH
Ligand information
Ligand IDLY4
InChIInChI=1S/C28H28N4O3/c1-30(2)15-18-11-12-31-16-21(19-7-3-5-9-23(19)31)25-26(28(34)29-27(25)33)22-17-32(13-14-35-18)24-10-6-4-8-20(22)24/h3-10,16-18H,11-15H2,1-2H3,(H,29,33,34)/t18-/m0/s1
InChIKeyZCBUQCWBWNUWSU-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(C)C[C@@H]1CCn2cc(c3ccccc23)C4=C(C(=O)NC4=O)c5cn(CCO1)c6ccccc56
ACDLabs 10.04O=C6NC(=O)C=5c1cn(c2ccccc12)CCOC(CN(C)C)CCn4c3ccccc3c(c4)C=56
OpenEye OEToolkits 1.5.0CN(C)C[C@@H]1CCn2cc(c3c2cccc3)C4=C(c5cn(c6c5cccc6)CCO1)C(=O)NC4=O
OpenEye OEToolkits 1.5.0CN(C)CC1CCn2cc(c3c2cccc3)C4=C(c5cn(c6c5cccc6)CCO1)C(=O)NC4=O
CACTVS 3.341CN(C)C[CH]1CCn2cc(c3ccccc23)C4=C(C(=O)NC4=O)c5cn(CCO1)c6ccccc56
FormulaC28 H28 N4 O3
Name(9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE;
LY333531
ChEMBLCHEMBL91829
DrugBankDB11829
ZINCZINC000003812168
PDB chain2j2i Chain B Residue 1307 [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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PDB2j2i A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L44 F49 V52 A65 L120 E121 R122 V126 D128 E171 L174 D186
Binding residue
(residue number reindexed from 1)		L12 F17 V20 A33 L88 E89 R90 V94 D96 E139 L142 D154
Annotation score1
Binding affinityMOAD: ic50=0.2uM
PDBbind-CN: -logKd/Ki=6.70,IC50=200nM
BindingDB: Kd=270nM,IC50=200nM
Enzymatic activity
Catalytic site (original residue number in PDB) N172 D186 L193
Catalytic site (residue number reindexed from 1) N140 D154 L161
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:0008134 transcription factor binding
GO:0030145 manganese ion binding
GO:0043024 ribosomal small subunit binding
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006915 apoptotic process
GO:0016310 phosphorylation
GO:0022898 regulation of transmembrane transporter activity
GO:0043066 negative regulation of apoptotic process
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0045824 negative regulation of innate immune response
GO:0045893 positive regulation of DNA-templated transcription
GO:0046777 protein autophosphorylation
GO:0050821 protein stabilization
GO:0060045 positive regulation of cardiac muscle cell proliferation
GO:0070561 vitamin D receptor signaling pathway
GO:0071346 cellular response to type II interferon
GO:0090336 positive regulation of brown fat cell differentiation
GO:1902033 regulation of hematopoietic stem cell proliferation
GO:1904263 positive regulation of TORC1 signaling
GO:1905062 positive regulation of cardioblast proliferation
GO:1990748 cellular detoxification
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2j2i, PDBe:2j2i, PDBj:2j2i
PDBsum2j2i
PubMed18077363
UniProtP11309|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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