Structure of PDB 5ek3 Chain A Binding Site BS02

Receptor Information
>5ek3 Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEK
LNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPY
CQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSK
GFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKAL
QVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAG
GSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLE
SNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQ
GGTDLMNFLKTVRSTTEKSLLKEG
Ligand information
Ligand ID5PK
InChIInChI=1S/C18H22N2O/c21-18(13-6-2-1-3-7-13)10-16-14-8-4-5-9-15(14)17-11-19-12-20(16)17/h4-5,8-9,11-13,16,18,21H,1-3,6-7,10H2/t16-,18+/m0/s1
InChIKeyYTRRAUACYORZLX-FUHWJXTLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[C@H](C[C@@H]1n2cncc2c3ccccc13)C4CCCCC4
OpenEye OEToolkits 2.0.4c1ccc2c(c1)-c3cncn3[C@H]2C[C@H](C4CCCCC4)O
OpenEye OEToolkits 2.0.4c1ccc2c(c1)-c3cncn3C2CC(C4CCCCC4)O
CACTVS 3.385O[CH](C[CH]1n2cncc2c3ccccc13)C4CCCCC4
FormulaC18 H22 N2 O
Name(1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol
ChEMBLCHEMBL3752711
DrugBank
ZINCZINC000095616584
PDB chain5ek3 Chain A Residue 502 [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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PDB5ek3 Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1
Resolution2.209 Å
Binding residue
(original residue number in PDB)		C129 V130 F163 F164 R231 G262 A264
Binding residue
(residue number reindexed from 1)		C118 V119 F152 F153 R220 G251 A253
Annotation score1
Binding affinityMOAD: ic50=38nM
BindingDB: IC50=<1000nM,Kd=3300nM,EC50=61nM,Ki=7.2nM
Enzymatic activity
Enzyme Commision number 1.13.11.52: indoleamine 2,3-dioxygenase.
Gene Ontology
Molecular Function
GO:0004833 tryptophan 2,3-dioxygenase activity
GO:0009055 electron transfer activity
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0020037 heme binding
GO:0033754 indoleamine 2,3-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0002376 immune system process
GO:0002666 positive regulation of T cell tolerance induction
GO:0002678 positive regulation of chronic inflammatory response
GO:0002830 positive regulation of type 2 immune response
GO:0006569 tryptophan catabolic process
GO:0006954 inflammatory response
GO:0007565 female pregnancy
GO:0019441 tryptophan catabolic process to kynurenine
GO:0019805 quinolinate biosynthetic process
GO:0032496 response to lipopolysaccharide
GO:0032693 negative regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0033555 multicellular organismal response to stress
GO:0034276 kynurenic acid biosynthetic process
GO:0034354 'de novo' NAD biosynthetic process from tryptophan
GO:0036269 swimming behavior
GO:0042098 T cell proliferation
GO:0042130 negative regulation of T cell proliferation
GO:0043065 positive regulation of apoptotic process
GO:0046006 regulation of activated T cell proliferation
GO:0070233 negative regulation of T cell apoptotic process
GO:0070234 positive regulation of T cell apoptotic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030485 smooth muscle contractile fiber
GO:0032421 stereocilium bundle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ek3, PDBe:5ek3, PDBj:5ek3
PDBsum5ek3
PubMed26642377
UniProtP14902|I23O1_HUMAN Indoleamine 2,3-dioxygenase 1 (Gene Name=IDO1)

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