Structure of PDB 6ykd Chain A Binding Site BS01

Receptor Information
>6ykd Chain A (length=277) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWG
ELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQD
LFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLN
RGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSL
GILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDR
PTFEEIQNHPWMQDVLLPQETAEIHLH
Ligand information
Ligand IDOWB
InChIInChI=1S/C22H23N5O2/c1-15(28)25-18-5-2-6-19(12-18)29-21-13-20(17-4-3-9-24-14-17)26-22(27-21)16-7-10-23-11-8-16/h2,5-8,10-13,17,24H,3-4,9,14H2,1H3,(H,25,28)/t17-/m1/s1
InChIKeyKUZQQGDXOKMLJL-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)Nc1cccc(Oc2cc(nc(n2)c3ccncc3)[CH]4CCCNC4)c1
CACTVS 3.385CC(=O)Nc1cccc(Oc2cc(nc(n2)c3ccncc3)[C@@H]4CCCNC4)c1
OpenEye OEToolkits 2.0.7CC(=O)Nc1cccc(c1)Oc2cc(nc(n2)c3ccncc3)C4CCCNC4
OpenEye OEToolkits 2.0.7CC(=O)Nc1cccc(c1)Oc2cc(nc(n2)c3ccncc3)[C@@H]4CCCNC4
FormulaC22 H23 N5 O2
Name~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide
ChEMBL
DrugBank
ZINC
PDB chain6ykd Chain A Residue 400 [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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PDB6ykd Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		L44 A65 K67 E121 V126 D128 L174 I185
Binding residue
(residue number reindexed from 1)		L16 A37 K39 E93 V98 D100 L146 I157
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1) D139 K141 N144 D158 L165 T176
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:6ykd, PDBe:6ykd, PDBj:6ykd
PDBsum6ykd
PubMed33448694
UniProtP11309|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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