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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGH AFFINITY HETERODIMER OF HIF2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS IN COMPLEX WITH A TETRAZOLE-CONTAINING ANTAGONIST
 
Authors :  T. H. Scheuermann, K. H. Gardner
Date :  22 Jan 15  (Deposition) - 09 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcription Factor, Hypoxia Inducible Factor, Inhibitor, Cancer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Scheuermann, D. Stroud, C. E. Sleet, L. Bayeh, C. Shokri, H. Wang, C. G. Caldwell, J. Longgood, J. B. Macmillan, R. K. Bruick, K. H. Gardner, U. K. Tambar
Isoform-Selective And Stereoselective Inhibition Of Hypoxia Inducible Factor-2.
J. Med. Chem. V. 58 5930 2015
PubMed-ID: 26226049  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00529

(-) Compounds

Molecule 1 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS-GB1 CON29
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL PAS DOMAIN (UNP RESIDUES 342-456)
    Gene: ARNT, BHLHE2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, BHLHE2,DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1-BETA, HIF1-BETA
 
Molecule 2 - ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS-GB1 CON30
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL PAS DOMAIN (UNP RESIDUES 239-350)
    Gene: EPAS1, BHLHE73, HIF2A, MOP2, PASD2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPAS-1, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 73, BHLHE73, HIF-1-ALPHA-LIKE FACTOR, HLF, HYPOXIA-INDUCIBLE FACTOR 2-ALPHA, HIF2-ALPHA, MEMBER OF PAS PROTEIN 2, PAS DOMAIN-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
143L2Ligand/Ion(5S,7R)-5,7-BIS(3-BROMOPHENYL)-4,5,6,7-TETRAHYDROTETRAZOLO[1,5-A]PYRIMIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
143L1Ligand/Ion(5S,7R)-5,7-BIS(3-BROMOPHENYL)-4,5,6,7-TETRAHYDROTETRAZOLO[1,5-A]PYRIMIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
143L1Ligand/Ion(5S,7R)-5,7-BIS(3-BROMOPHENYL)-4,5,6,7-TETRAHYDROTETRAZOLO[1,5-A]PYRIMIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:248 , MET A:252 , PHE A:280 , TYR A:281 , MET A:289 , SER A:292 , HIS A:293 , VAL A:302 , TYR A:307 , GLY A:323 , ASN A:341 , HOH A:505binding site for residue 43L A 401
2AC2SOFTWAREHIS C:248 , MET C:252 , TYR C:281 , MET C:289 , SER C:292 , HIS C:293 , VAL C:302 , TYR C:307 , GLY C:323 , CYS C:339 , ASN C:341 , HOH C:515 , HOH C:519binding site for residue 43L C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XT2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XT2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XT2)

(-) Exons   (0, 0)

(no "Exon" information available for 4XT2)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeeee.....eeee..hhhhhh..hhhhhh..hhhhh....hhhhhhhhhhhhhhhheee...eeee.....eeeeeeeeeeee......eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4xt2 A 234 GEFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK 349
                                   243       253       263       273       283       293       303       313       323       333       343      


Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....eeee..hhhhhhh.hhhhhh..hhhhhh...hhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeeeeee.........eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4xt2 B 358 CQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSS 468
                                   367       377       387       397       407       417       427       437       447       457       467 


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh.eeeeee.....eeee..hhhhhhh.hhhhh...hhhhh....hhhhhhhhhhhhhhhheee...eeee.....eeeeeeeeeeee......eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4xt2 C 236 FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK 349
                                   245       255       265       275       285       295       305       315       325       335       345    


Chain D from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeee..hhhhhhh.hhhhhh..hhhhhh...hhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4xt2 D 360 PTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKN 466
                                   369       379       389       399       409       419       429       439       449       459
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4XT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XT2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XT2)

(-) Gene Ontology  (60, 79)

Asymmetric Unit(hide GO term definitions)

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  4xt2
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  ARNT_HUMAN | P27540
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  EPAS1_HUMAN | Q99814
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARNT_HUMAN | P27540: 1d7g 1x0o 2a24 2arn 2b02 2hv1 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4ghi 4gs9 4h6j 4lpz 4pky 5nj8 5tbm 5ufp 5v0l
        EPAS1_HUMAN | Q99814: 1p97 2a24 3f1n 3f1o 3f1p 3h7w 3h82 4ghi 4gs9 4pky 5kiz 5tbm 5ufp

(-) Related Entries Specified in the PDB File

3f1o HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH THE HIF-2 ALPHA PAS-B INTERNAL CAVITY OCCUPIED BY A MEDICINAL CHEMISTRY- OPTIMIZED SMALL MOLECULE IDENTIFIED FROM AN NMR SCREEN OF A DRUG FRAGMENT LIBRARY
3f1p HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH WATER IN THE HIF-2 ALPHA PAS-B INTERNAL CAVITY
3h82 HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH THE HIF-2 ALPHA PAS-B INTERNAL CAVITY OCCUPIED BY A MEDICINAL CHEMISTRY- OPTIMIZED SMALL MOLECULE IDENTIFIED FROM AN NMR SCREEN OF A DRUG FRAGMENT LIBRARY
3hw7 HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH THE HIF-2 ALPHA PAS-B INTERNAL CAVITY OCCUPIED BY A MEDICINAL CHEMISTRY- OPTIMIZED SMALL MOLECULE IDENTIFIED FROM AN NMR SCREEN OF A DRUG FRAGMENT LIBRARY
4ghi HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH THE HIF-2 ALPHA PAS-B INTERNAL CAVITY OCCUPIED BY A MEDICINAL CHEMISTRY- OPTIMIZED SMALL MOLECULE IDENTIFIED FROM AN HTS SCREEN OF PROTEIN HETERODIMER DISRUPTION THAT ATTENUATES HIF TRANSCRIPTION IN CELLS
4gs9 HIF2 ALPHA/ARNT C-TERMINAL PAS DOMAIN HETERODIMER WITH THE HIF-2 ALPHA PAS-B INTERNAL CAVITY OCCUPIED BY AN INACTIVE ANALOG OF THE SMALL MOLECULE IN PDB ENTRY 4GHI
4lpz ARNT PAS-B DOMAIN IN COMPLEX WITH A COILED-COIL COACTIVATER