Structure of PDB 4dtk Chain A Binding Site BS01

Receptor Information
>4dtk Chain A (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
YDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFE
EIQNHPWMQDVLLPQETAEIHLH
Ligand information
Ligand ID7LI
InChIInChI=1S/C18H23N3O3S/c1-11(2)24-14-7-3-5-12(9-15-17(22)20-18(23)25-15)16(14)21-8-4-6-13(19)10-21/h3,5,7,9,11,13H,4,6,8,10,19H2,1-2H3,(H,20,22,23)/b15-9-/t13-/m1/s1
InChIKeyULMRMVZQMKZWKJ-MLJKTZRHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)Oc1cccc(C=C2SC(=O)NC2=O)c1N3CCC[CH](N)C3
CACTVS 3.370CC(C)Oc1cccc(\C=C2/SC(=O)NC2=O)c1N3CCC[C@@H](N)C3
ACDLabs 12.01O=C1C(\SC(=O)N1)=C\c2cccc(OC(C)C)c2N3CCCC(N)C3
OpenEye OEToolkits 1.7.6CC(C)Oc1cccc(c1[N@]2CCC[C@H](C2)N)/C=C\3/C(=O)NC(=O)S3
OpenEye OEToolkits 1.7.6CC(C)Oc1cccc(c1N2CCCC(C2)N)C=C3C(=O)NC(=O)S3
FormulaC18 H23 N3 O3 S
Name(5Z)-5-{2-[(3R)-3-aminopiperidin-1-yl]-3-(propan-2-yloxy)benzylidene}-1,3-thiazolidine-2,4-dione
ChEMBLCHEMBL2048871
DrugBank
ZINCZINC000084670254
PDB chain4dtk Chain A Residue 408 [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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PDB4dtk Discovery of novel benzylidene-1,3-thiazolidine-2,4-diones as potent and selective inhibitors of the PIM-1, PIM-2, and PIM-3 protein kinases.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		L44 A65 K67 L120 V126 L174 I185 D186
Binding residue
(residue number reindexed from 1)		L12 A33 K35 L88 V94 L142 I153 D154
Annotation score1
Binding affinityMOAD: ic50<0.004uM
PDBbind-CN: -logKd/Ki=8.52,IC50<0.003uM
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:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0043066 negative regulation of apoptotic process

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Molecular Function
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Biological Process
External links
PDB RCSB:4dtk, PDBe:4dtk, PDBj:4dtk
PDBsum4dtk
PubMed22727640
UniProtP11309|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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