Structure of PDB 6o3i Chain B Binding Site BS02

Receptor Information
>6o3i Chain B (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRE
RVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNI
AVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDG
DCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCL
EKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPK
EFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFL
CSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIP
ASQGGTDLMNFLKTVRSTTEKSLLK
Ligand information
Ligand IDLKP
InChIInChI=1S/C18H21FN2O2/c19-14-3-1-2-13-16-9-20-10-21(16)15(18(13)14)8-17(23)11-4-6-12(22)7-5-11/h1-3,9-12,15,17,22-23H,4-8H2/t11-,12-,15-,17+/m0/s1
InChIKeyYGACXVRLDHEXKY-WXRXAMBDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc-2c(c(c1)F)C(n3c2cnc3)CC(C4CCC(CC4)O)O
ACDLabs 12.01c23C(CC(O)C1CCC(CC1)O)n4c(c2cccc3F)cnc4
OpenEye OEToolkits 2.0.7c1cc-2c(c(c1)F)[C@@H](n3c2cnc3)C[C@H](C4CCC(CC4)O)O
CACTVS 3.385O[CH]1CC[CH](CC1)[CH](O)C[CH]2n3cncc3c4cccc(F)c24
CACTVS 3.385O[C@H]1CC[C@@H](CC1)[C@H](O)C[C@@H]2n3cncc3c4cccc(F)c24
FormulaC18 H21 F N2 O2
Nametrans-4-{(1R)-2-[(5S)-6-fluoro-5H-imidazo[5,1-a]isoindol-5-yl]-1-hydroxyethyl}cyclohexan-1-ol;
Navoximod
ChEMBLCHEMBL3989951
DrugBankDB15439
ZINC
PDB chain6o3i Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6o3i Discovery of Clinical Candidate (1R,4r)-4-((R)-2-((S)-6-Fluoro-5H-imidazo[5,1-a]isoindol-5-yl)-1-hydroxyethyl)cyclohexan-1-ol (Navoximod), a Potent and Selective Inhibitor of Indoleamine 2,3-Dioxygenase 1.
Resolution2.69 Å
Binding residue
(original residue number in PDB)		Y126 C129 V130 F163 F164 L234 G262 A264
Binding residue
(residue number reindexed from 1)		Y119 C122 V123 F156 F157 L227 G255 A257
Annotation score1
Binding affinityBindingDB: IC50=<1000nM,EC50=250nM,Ki=5.8nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6o3i, PDBe:6o3i, PDBj:6o3i
PDBsum6o3i
PubMed31264862
UniProtP14902|I23O1_HUMAN Indoleamine 2,3-dioxygenase 1 (Gene Name=IDO1)

[Back to BioLiP]