Structure of PDB 5ek4 Chain B Binding Site BS02

Receptor Information

>5ek4 Chain B (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVE
KLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVP
YCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCS
KGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKA
LQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFA
GGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSL
ESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQ
GGTDLMNFLKTVRSTTEKSLLKEG

Ligand information

Ligand ID

5PF

InChI

InChI=1S/C18H21FN2O/c19-14-8-4-7-13-16-10-20-11-21(16)15(18(13)14)9-17(22)12-5-2-1-3-6-12/h4,7-8,10-12,15,17,22H,1-3,5-6,9H2/t15-,17+/m0/s1

InChIKey

AKOIXTSNUPHRQM-DOTOQJQBSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.4	c1cc-2c(c(c1)F)C(n3c2cnc3)CC(C4CCCCC4)O
OpenEye OEToolkits 2.0.4	c1cc-2c(c(c1)F)[C@@H](n3c2cnc3)C[C@H](C4CCCCC4)O
CACTVS 3.385	O[C@H](C[C@@H]1n2cncc2c3cccc(F)c13)C4CCCCC4
CACTVS 3.385	O[CH](C[CH]1n2cncc2c3cccc(F)c13)C4CCCCC4

Formula

C18 H21 F N2 O

Name

(1~{R})-1-cyclohexyl-2-[(5~{S})-6-fluoranyl-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol

PDB chain

5ek4 Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5ek4 Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1
Resolution	2.64 Å
Binding residue (original residue number in PDB)	Y126 F163 F164 F226 R231 L234 G262 A264
Binding residue (residue number reindexed from 1)	Y116 F153 F154 F216 R221 L224 G252 A254
Annotation score	1
Binding affinity	BindingDB: IC50=<1000nM,EC50=200nM

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:5ek4, PDBe:5ek4, PDBj:5ek4
PDBsum	5ek4
PubMed	26642377
UniProt	P14902\|I23O1_HUMAN Indoleamine 2,3-dioxygenase 1 (Gene Name=IDO1)

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