Structure of PDB 3dcv Chain A Binding Site BS01

Receptor Information
>3dcv Chain A (length=274) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELP
NGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFD
FITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGE
LKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGIL
LYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTF
EEIQNHPWMQDVLLPQETAEIHLH
Ligand information
Ligand ID55E
InChIInChI=1S/C17H14N2O2/c1-11-9-13(7-8-16(11)20)15-10-14(18-17(21)19-15)12-5-3-2-4-6-12/h2-9,20H,10H2,1H3
InChIKeyAZXKZZMGLACNIJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341
OpenEye OEToolkits 1.5.0		Cc1cc(ccc1O)C2=NC(=O)N=C(C2)c3ccccc3
ACDLabs 10.04O=C2N=C(c1ccccc1)CC(=N2)c3ccc(O)c(c3)C
FormulaC17 H14 N2 O2
Name4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin-2(5H)-one
ChEMBL
DrugBankDB07151
ZINCZINC000039122795
PDB chain3dcv Chain A Residue 500 [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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PDB3dcv 4-(1H-indazol-5-yl)-6-phenylpyrimidin-2(1H)-one analogs as potent CDC7 inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		F49 A65 K67 L120 E121 R122 L174 I185 D186
Binding residue
(residue number reindexed from 1)		F18 A34 K36 L89 E90 R91 L143 I154 D155
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.52,IC50=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1) D136 K138 N141 D155 L162 T173
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:3dcv, PDBe:3dcv, PDBj:3dcv
PDBsum3dcv
PubMed18672368
UniProtP11309|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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