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(-) Description

Title :  STRUCTURE OF PREGNANE X RECEPTOR IN COMPLEX WITH A SPHINGOSINE 1-PHOSPHATE RECEPTOR 1 ANTAGONIST
 
Authors :  Y. Xue, L. Oster
Date :  13 Jul 15  (Deposition) - 21 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Signaling Protein, Pxr Ligand, Pxr Agonist, Cyp3A4 Induction, Nuclear Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. J. Hennessy, V. B. Oza, A. Adam, K. Byth, L. Castriotta, G. Grewal, G. Hamilton, V. M. Kamhi, P. Lewis, D. Li, P. D. Lyne, L. Oster, M. T. Rooney, J. C. Saeh, L. Sha, Q. Su, S. Wen, Y. Xue, B. Yang
Identification And Optimization Of Benzimidazole Sulfonamides As Orally Bioavailable Sphingosine 1-Phosphate Receptor 1 Antagonists With In Vivo Activity.
J. Med. Chem. V. 58 7057 2015
PubMed-ID: 26291341  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01078

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymORPHAN NUCLEAR RECEPTOR PAR1, ORPHAN NUCLEAR RECEPTOR PXR, PREGNANE X RECEPTOR, STEROID AND XENOBIOTIC RECEPTOR, SXR, STEROID RECEPTOR COACTIVATOR 1
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 1
    ChainsC, D
    EC Number2.3.1.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID RECEPTOR COACTIVATOR 1, SRC-1, STEROID RECEPTOR COACTIVATOR 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1D7E2Ligand/Ion4-CHLORO-N-[(1R)-1-[1-ETHYL-6-(TRIFLUOROMETHYL)BENZIMIDAZOL-2-YL]ETHYL]BENZENESULFONAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:209 , VAL A:211 , HIS A:242 , MET A:243 , MET A:246 , PHE A:281 , GLN A:285 , PHE A:288 , TRP A:299 , TYR A:306 , MET A:323 , HIS A:327BINDING SITE FOR RESIDUE D7E A1433
2AC2SOFTWARELEU B:209 , VAL B:211 , HIS B:242 , MET B:243 , PHE B:281 , GLN B:285 , PHE B:288 , TRP B:299 , TYR B:306 , MET B:323 , HIS B:327 , HIS B:407BINDING SITE FOR RESIDUE D7E B1432

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A86)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys B:207 -Ser B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A86)

(-) Exons   (0, 0)

(no "Exon" information available for 5A86)

(-) Sequences/Alignments

Asymmetric/Biological 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh....eeeee.....eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhee....eeee..eeee......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a86 A 143 LTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVEEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGIT 432
                                   152       162       172    || 198       208       218       228       238       248       258       268       278       288       298       308   ||  321       331       341       351       361       371       381       391       401       411       421       431 
                                                            177|                                                                                                                   312|                                                                                                                    
                                                             194                                                                                                                    316                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh....eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhee....eeee..eeeee..hhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a86 B 141 QGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGI 431
                                   150       160       170      |194       204       214       224       234       244       254       264       274       284       294       304     ||317       327       337       347       357       367       377       387       397       407       417       427    
                                                              177|                                                                                                                   310|                                                                                                                     
                                                               192                                                                                                                    314                                                                                                                     

Chain C from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5a86 C 682 SLTERHKILHRLLQE 696
                                   691     

Chain D from PDB  Type:PROTEIN  Length:17
                                                 
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 5a86 D 682 SLTERHKILHRLLQEGS 698
                                   691       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5A86)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A86)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A86)

(-) Gene Ontology  (77, 87)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA1_HUMAN | Q157881fm6 1fm9 1k4w 1k74 1k7l 1kv6 1n4h 1nq7 1nrl 1p8d 1pzl 1rdt 1tfc 1u3r 1u3s 1x76 1x78 1x7b 1x7j 1xiu 1xv9 1xvp 1yy4 1yye 1zaf 2a3i 2c52 2fvj 2gtk 2hbh 2hc4 2hcd 2hfp 2npa 2nv7 2p54 2prg 3bej 3bqd 3ctb 3cwd 3dct 3dcu 3dr1 3et1 3et3 3fei 3fej 3fur 3fxv 3g8i 3g9e 3gyt 3gyu 3h0a 3hc5 3hc6 3hvl 3ipq 3ips 3ipu 3kmr 3lmp 3okh 3oki 3olf 3oll 3ols 3omk 3omm 3omo 3omp 3omq 3oof 3ook 3p88 3p89 3qt0 3rut 3ruu 3rvf 3s9s 3t03 3uu7 3uua 3uud 3v9y 3vn2 4dk7 4dk8 4dm6 4dm8 4dqm 4f9m 4fgy 4g1d 4g1y 4g1z 4g20 4g21 4g2h 4hee 4j5w 4j5x 4jyg 4jyh 4jyi 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4ruj 4rup 4tuz 4tv1 4uda 4udb 4y29 5avi 5avl 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w
        NR1I2_HUMAN | O754691ilg 1ilh 1m13 1nrl 1skx 2o9i 2qnv 3ctb 3hvl 3r8d 4j5w 4j5x 4ny9 4s0s 4s0t 4x1f 4x1g 4xao 4xhd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5A86)