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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INDOLEAMINE 2,3-DIOXYGENAGSE 1 (IDO1) COMPLEXED WITH NLG919 ANALOGUE
 
Authors :  Y. H. Peng, J. S. Wu, S. Y. Wu
Date :  03 Nov 15  (Deposition) - 23 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inhibitor, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Peng, S. H. Ueng, C. T. Tseng, M. S. Hung, J. S. Song, J. S. Wu, F. Y. Liao, Y. S. Fan, M. H. Wu, W. C. Hsiao, C. C. Hsueh, S. Y. Lin, C. Y. Cheng, C. H. Tu, L. C. Lee, M. F. Cheng, K. S. Shia, C. Shih, S. Y. Wu
Important Hydrogen Bond Networks In Indoleamine 2, 3-Dioxygenase 1 (Ido1) Inhibitor Design Revealed By Crystal Structures Of Imidazoleisoindole Derivatives With Ido1
J. Med. Chem. V. 59 282 2016
PubMed-ID: 26642377  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01390

(-) Compounds

Molecule 1 - INDOLEAMINE 2,3-DIOXYGENASE 1
    Chains: A, B
    EC Number: 1.13.11.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: IDO1, IDO, INDO
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDO-1,INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15PJ2Ligand/Ion1-CYCLOHEXYL-2-[(5~{S})-6-FLUORANYL-5~{H}-IMIDAZO[1,5-B]ISOINDOL-5-YL]ETHANONE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
15PJ1Ligand/Ion1-CYCLOHEXYL-2-[(5~{S})-6-FLUORANYL-5~{H}-IMIDAZO[1,5-B]ISOINDOL-5-YL]ETHANONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
15PJ1Ligand/Ion1-CYCLOHEXYL-2-[(5~{S})-6-FLUORANYL-5~{H}-IMIDAZO[1,5-B]ISOINDOL-5-YL]ETHANONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:163 , SER A:167 , VAL A:170 , PHE A:214 , ILE A:217 , PHE A:226 , SER A:263 , ALA A:264 , PHE A:270 , PHE A:291 , ARG A:343 , HIS A:346 , ILE A:349 , VAL A:350 , LEU A:388 , VAL A:391 , 5PJ A:502 , HOH A:621binding site for residue HEM A 501
2AC2SOFTWARECYS A:129 , VAL A:130 , PHE A:163 , GLY A:262 , SER A:263 , ALA A:264 , HEM A:501binding site for residue 5PJ A 502
3AC3SOFTWAREPHE B:163 , SER B:167 , VAL B:170 , PHE B:214 , PHE B:226 , SER B:263 , ALA B:264 , PHE B:270 , PHE B:291 , ARG B:343 , HIS B:346 , ILE B:349 , VAL B:350 , TYR B:353 , ILE B:354 , VAL B:391 , 5PJ B:502 , HOH B:603binding site for residue HEM B 501
4AC4SOFTWARECYS B:129 , VAL B:130 , PHE B:163 , SER B:167 , LEU B:234 , GLY B:262 , SER B:263 , ALA B:264 , HEM B:501binding site for residue 5PJ B 502

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:308 -B:308

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EK2)

(-) Exons   (0, 0)

(no "Exon" information available for 5EK2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eee...eeeee.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ek2 A  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQGGTDLMNFLKTVRSTTEKSLLKEG 403
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361|      389       399    
                                                                                                                                                                                                                                                                                                                                                                                       361|                       
                                                                                                                                                                                                                                                                                                                                                                                        380                       


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhh.....hhhhhh....ee.......hhh.ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............ee.............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ek2 B  12 SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQEAKGTGGTDLMNFLKTVRSTTEKSLLKEG 403
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       375       385       395        
                                                                                                                                                                                                                                                                                                                                                                                      360|                            
                                                                                                                                                                                                                                                                                                                                                                                       375
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EK2)

(-) Gene Ontology  (32, 32)

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 Related Entries

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UniProtKB/Swiss-Prot
        I23O1_HUMAN | P14902: 2d0t 2d0u 4pk5 4pk6 4u72 4u74 5ek3 5ek4 5etw 5xe1

(-) Related Entries Specified in the PDB File

5ek3 5ek4