Structure of PDB 3vbw Chain A Binding Site BS01

Receptor Information
>3vbw Chain A (length=264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESQYQVGPLLGGSVYSGIRVSDNLPVAIKHVEKDRISDWGELTRVPMEVV
LLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQE
ELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGA
LLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIP
FEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQ
DVLLPQETAEIHLH
Ligand information
Ligand ID0FN
InChIInChI=1S/C10H5NO2/c11-5-8-9(12)6-3-1-2-4-7(6)10(8)13/h1-4,8H
InChIKeyGKEKUQYTCADDSQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O=C1C(C#N)C(=O)c2ccccc12
ACDLabs 12.01O=C2c1ccccc1C(=O)C2C#N
OpenEye OEToolkits 1.7.6c1ccc2c(c1)C(=O)C(C2=O)C#N
FormulaC10 H5 N O2
Name1,3-dioxo-2,3-dihydro-1H-indene-2-carbonitrile
ChEMBLCHEMBL2032370
DrugBank
ZINCZINC000100102142
PDB chain3vbw Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vbw Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.
Resolution2.48 Å
Binding residue
(original residue number in PDB)		L44 V52 A65 K67 E121 L174 I185 D186
Binding residue
(residue number reindexed from 1)		L10 V14 A27 K29 E80 L133 I144 D145
Annotation score1
Binding affinityMOAD: ic50=6uM
PDBbind-CN: -logKd/Ki=5.22,IC50=6uM
BindingDB: IC50=6000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1) D126 K128 N131 D145 L152 T163
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
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Biological Process
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Cellular Component
External links
PDB RCSB:3vbw, PDBe:3vbw, PDBj:3vbw
PDBsum3vbw
PubMed22339127
UniProtP11309|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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