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(-) Description

Title :  DISCOVERY OF NOVEL, ORALLY EFFICACIOUS LIVER X RECEPTOR (LXR) BETA AGONISTS
 
Authors :  G. Chen, B. M. Mckeever
Date :  12 Feb 16  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  E,F  (1x)
Keywords :  Lxrbeta-Lbd, Rxrbeta-Lbd, Heterodimer, Agonist, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zheng, L. Zhuang, K. Y. Fan, C. M. Tice, W. Zhao, C. Dong, S. D. Lotesta K. Leftheris, P. R. Lindblom, Z. Liu, J. Shimada, P. B. Noto, S. Meng, A. Hardy, L. Howard, P. Krosky, J. Guo, K. Lipinski, G. Kandpal, Y. Bukhtiyarov, Y. Zhao, D. Lala, R. Van Orden, J. Zhou, G. Chen, Z. Wu, B. M. Mckeever, G. M. Mcgeehan, R. E. Gregg, D. A. Claremon, S. B. Singh
Discovery Of A Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonist.
J. Med. Chem. V. 59 3264 2016
PubMed-ID: 26990539  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B02029

(-) Compounds

Molecule 1 - OXYSTEROLS RECEPTOR LXR-BETA,NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NR1H2, LXRB, NER, UNR, NCOA2, BHLHE75, SRC2, TIF2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LIVER X RECEPTOR BETA,NUCLEAR RECEPTOR NER,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 2,UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR, NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75,BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2
 
Molecule 2 - RETINOIC ACID RECEPTOR RXR-BETA,NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RXRB, NR2B2, NCOA2, BHLHE75, SRC2, TIF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 2,RETINOID X RECEPTOR BETA,NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75, BHLHE75,TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEF
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   EF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
167S2Ligand/Ion{2-[(2R)-4-[4-(HYDROXYMETHYL)-3-(METHYLSULFONYL)PHENYL]-2-(PROPAN-2-YL)PIPERAZIN-1-YL]-4-(TRIFLUOROMETHYL)PYRIMIDIN-5-YL}METHANOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
167S1Ligand/Ion{2-[(2R)-4-[4-(HYDROXYMETHYL)-3-(METHYLSULFONYL)PHENYL]-2-(PROPAN-2-YL)PIPERAZIN-1-YL]-4-(TRIFLUOROMETHYL)PYRIMIDIN-5-YL}METHANOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
167S1Ligand/Ion{2-[(2R)-4-[4-(HYDROXYMETHYL)-3-(METHYLSULFONYL)PHENYL]-2-(PROPAN-2-YL)PIPERAZIN-1-YL]-4-(TRIFLUOROMETHYL)PYRIMIDIN-5-YL}METHANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:268 , PHE A:271 , THR A:272 , LEU A:274 , SER A:278 , GLU A:281 , MET A:312 , THR A:316 , ARG A:319 , PHE A:329 , LEU A:330 , LEU A:345 , HIS A:435 , HOH A:601binding site for residue 67S A 501
2AC2SOFTWAREPHE E:268 , PHE E:271 , THR E:272 , LEU E:274 , SER E:278 , GLU E:281 , MET E:312 , THR E:316 , PHE E:329 , LEU E:330 , PHE E:340 , LEU E:345 , HIS E:435 , LEU E:449binding site for residue 67S E 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I4V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I4V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I4V)

(-) Exons   (0, 0)

(no "Exon" information available for 5I4V)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee...eeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i4v A 218 VQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPASGSASQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVHEGSGSGSHKILHRLLQD 477
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeehhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i4v B 297 EEMPVDRILEAELAVEPVTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIPIDTFLMEMLEAKILHRLLQ 543
                                   306     ||338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508    || 521      |538     
                                         312|                                                                                                                                                                               513|        528|       
                                          335                                                                                                                                                                                517         536       


Chain E from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee...eeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i4v E 218 VQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGSASQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQDKKLPPLLSEIWDVKILHRLLQD 477
                                   227       237       247      |263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     ||472     
                                                              254|                                                                                                                                                                                                   459|        
                                                               261                                                                                                                                                                                                    469        


Chain F from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeehhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i4v F 297 EEMPVDRILEAELAVEPVTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTFLMEMLEAGSHKILHRLLQD 544
                                   306     ||338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508     ||522     ||536        
                                         312|                                                                                                                                                                                514|      528|           
                                          335                                                                                                                                                                                 519       533
   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 5I4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I4V)

(-) Gene Ontology  (98, 131)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d
        NR1H2_HUMAN | P55055: 1p8d 1pq6 1pq9 1pqc 1upv 1upw 3kfc 3l0e 4dk7 4dk8 4nqa 4rak 5hjp 5jy3 5kya 5kyj
        RXRB_HUMAN | P28702: 1h9u 1uhl 5hjp 5kya 5kyj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I4V)