Structure of PDB 3vc4 Chain A Binding Site BS01
Receptor Information
>3vc4 Chain A (length=274) Species:
9606
(Homo sapiens) [
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PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPN
GTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDF
ITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGEL
KLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILL
YDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFE
EIQNHPWMQDVLLPQETAEIHLHS
Ligand information
Ligand ID
0FS
InChI
InChI=1S/C11H6F3NO2S/c12-11(13,14)7-3-1-2-6(4-7)5-8-9(16)15-10(17)18-8/h1-5H,(H,15,16,17)/b8-5-
InChIKey
NGJLOFCOEOHFKQ-YVMONPNESA-N
SMILES
Software
SMILES
CACTVS 3.370
FC(F)(F)c1cccc(C=C2SC(=O)NC2=O)c1
ACDLabs 12.01
O=C1C(\SC(=O)N1)=C\c2cccc(c2)C(F)(F)F
OpenEye OEToolkits 1.7.6
c1cc(cc(c1)C(F)(F)F)C=C2C(=O)NC(=O)S2
OpenEye OEToolkits 1.7.6
c1cc(cc(c1)C(F)(F)F)/C=C\2/C(=O)NC(=O)S2
CACTVS 3.370
FC(F)(F)c1cccc(\C=C\2SC(=O)NC\2=O)c1
Formula
C11 H6 F3 N O2 S
Name
(5Z)-5-[3-(trifluoromethyl)benzylidene]-1,3-thiazolidine-2,4-dione
ChEMBL
CHEMBL183906
DrugBank
ZINC
ZINC000012576047
PDB chain
3vc4 Chain A Residue 1 [
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Receptor-Ligand Complex Structure
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PDB
3vc4
Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.
Resolution
2.23 Å
Binding residue
(original residue number in PDB)
L44 V52 K67 R122 L174 I185 D186
Binding residue
(residue number reindexed from 1)
L12 V20 K35 R90 L142 I153 D154
Annotation score
1
Binding affinity
MOAD
: ic50=24nM
PDBbind-CN
: -logKd/Ki=7.62,IC50=24nM
BindingDB: IC50=17nM
Enzymatic activity
Catalytic site (original residue number in PDB)
D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1)
D135 K137 N140 D154 L161 T172
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:3vc4
,
PDBe:3vc4
,
PDBj:3vc4
PDBsum
3vc4
PubMed
22339127
UniProt
P11309
|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)
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