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(-) Description

Title :  STRUCTURE-ACTIVITY RELATIONSHIP STUDY OF VITAMIN D ANALOGS WITH OXOLANE GROUP IN THEIR SIDE CHAIN
 
Authors :  N. Rochel, A. Y. Belorusova
Date :  03 Apr 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Y. Belorusova, A. Martinez, Z. Gandara, G. Gomez, Y. Fall, N. Rochel
Structure-Activity Relationship Study Of Vitamin D Analogs With Oxolane Group In Their Side Chain.
Eur J Med Chem V. 134 86 2017
PubMed-ID: 28399453  |  Reference-DOI: 10.1016/J.EJMECH.2017.03.081

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VDRA, NR1I1A, VDR
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: VDR-A,1,25-DIHYDROXYVITAMIN D3 RECEPTOR A,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1-A
 
Molecule 2 - SRC1
    Chains: B
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
191W1Ligand/Ion(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{A}~{S},7~{A}~{R})-7~{A}-METHYL-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-OXIDANYLPROPAN-2-YL)OXOLAN-2-YL]ETHYL]-2,3,3~{A},5,6,7-HEXAHYDRO-1~{H}-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
191W1Ligand/Ion(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{A}~{S},7~{A}~{R})-7~{A}-METHYL-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-OXIDANYLPROPAN-2-YL)OXOLAN-2-YL]ETHYL]-2,3,3~{A},5,6,7-HEXAHYDRO-1~{H}-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
191W-1Ligand/Ion(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{A}~{S},7~{A}~{R})-7~{A}-METHYL-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-OXIDANYLPROPAN-2-YL)OXOLAN-2-YL]ETHYL]-2,3,3~{A},5,6,7-HEXAHYDRO-1~{H}-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-CYCLOHEXANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:175 , SER A:265 , ILE A:296 , ILE A:299 , ARG A:302 , SER A:303 , SER A:306 , TRP A:314 , CYS A:316 , VAL A:328 , HIS A:333 , HIS A:423binding site for residue 91W A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NKY)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nky A 155 MLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV 452
                                   164       174       184     ||254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        
                                                             190|                                                                                                                                                                                                         
                                                              251                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5nky B 686 RHKILHRLLQ 695
                                   695
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5NKY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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 Related Entries

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

UniProtKB/Swiss-Prot
        VDRA_DANRE | Q9PTN2: 2hbh 2hc4 2hcd 3dr1 3o1d 3o1e 4fhh 4fhi 4g1d 4g1y 4g1z 4g20 4g21 4g2h 4ia1 4ia2 4ia3 4ia7 4q0a 4ruj 4ruo 4rup 5e7v 5lga 5nma

(-) Related Entries Specified in the PDB File

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