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(-) Description

Title :  STRUCTURE OF PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN (PHD) WITH INHIBITORS
 
Authors :  Y. Ma, L. Yang
Date :  03 Apr 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Prolyl Hydroxylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Deng, B. Zhao, Y. Ma, Q. Xu, H. Wang, L. Yang, Q. Zhang, T. B. Guo, W. Zhang, Y. Jiao, X. Cai, J. Zhang, H. Liu, X. Guan, H. Lu, J. Xiang, J. D. Elliott, X. Lin, F. Ren
Novel Complex Crystal Structure Of Prolyl Hydroxylase Domain-Containing Protein 2 (Phd2): 2, 8-Diazaspiro[4. 5]Decan-1-Ones As Potent, Orally Bioavailable Phd2 Inhibitors
Bioorg. Med. Chem. V. 21 6349 2013
PubMed-ID: 24055079  |  Reference-DOI: 10.1016/J.BMC.2013.08.046

(-) Compounds

Molecule 1 - EGL NINE HOMOLOG 1
    ChainsA
    EC Number1.14.11.29
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 189-399
    GeneC1ORF12, EGLN1, PNAS-118, PNAS-137
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE 2, HIF-PH2, HIF- PROLYL HYDROXYLASE 2, HPH-2, PROLYL HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2, PHD2, SM-20

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
14JR1Ligand/Ion2-(BIPHENYL-4-YL)-8-[(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]-2,8-DIAZASPIRO[4.5]DECAN-1-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:313 , ASP A:315 , HIS A:374 , 4JR A:402 , HOH A:537BINDING SITE FOR RESIDUE NI A 401
2AC2SOFTWARETYR A:303 , TYR A:310 , HIS A:313 , ASP A:315 , ARG A:322 , HIS A:374 , VAL A:376 , TRP A:389 , PHE A:391 , ARG A:396 , NI A:401 , EDO A:403 , HOH A:537BINDING SITE FOR RESIDUE 4JR A 402
3AC3SOFTWARETYR A:329 , LEU A:343 , ARG A:383 , 4JR A:402 , HOH A:539BINDING SITE FOR RESIDUE EDO A 403

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:201 -A:208

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZR)

(-) 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:204
                                                                                                                                                                                                                                            
               SCOP domains d4jzra_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhh...............eeeee......hhhhhhhhhhhhhhhhh.........eeee..eeeeee......eeee........eeeeeeee.....hhhhhh..eee........eee.....eeeeee......eee......eeeeeeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jzr A 189 PALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARA 399
                                   198       208       218       228       238   ||  255       265       275       285       295       305       315       325       335       345       355       365       375       385       395    
                                                                               242|                                                                                                                                                     
                                                                                250                                                                                                                                                     

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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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

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
        EGLN1_HUMAN | Q9GZT92g19 2g1m 2hbt 2hbu 2y33 2y34 3hqr 3hqu 3ouh 3oui 3ouj 4bqw 4bqx 4bqy 4kbz 4uwd 5a3u 5l9b 5l9r 5l9v 5la9 5las 5lat 5lb6 5lbb 5lbc 5lbe 5lbf 5v18

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JZR)