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(-) Description

Title :  STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE IN COMPLEX WITH N-METHYL-1-[3-(PYRIDIN-3-YL)PHENYL]METHANAMINE
 
Authors :  Y. Amano, T. Yamaguchi
Date :  10 Feb 15  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Inhibitor Complex, Hydrolase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Amano, E. Tanabe, T. Yamaguchi
Identification Of N-Ethylmethylamine As A Novel Scaffold Fo Inhibitors Of Soluble Epoxide Hydrolase By Crystallographic Fragment Screening
Bioorg. Med. Chem. V. 23 2310 2015
PubMed-ID: 25862210  |  Reference-DOI: 10.1016/J.BMC.2015.03.083

(-) Compounds

Molecule 1 - BIFUNCTIONAL EPOXIDE HYDROLASE 2
    ChainsA
    EC Number3.3.2.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-555
    GeneEPHX2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
13C51Ligand/IonN-METHYL-1-[3-(PYRIDIN-3-YL)PHENYL]METHANAMINE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13C52Ligand/IonN-METHYL-1-[3-(PYRIDIN-3-YL)PHENYL]METHANAMINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , ASP A:11 , ASP A:185 , ILE A:186binding site for residue MG A 601
2AC2SOFTWAREPHE A:267 , ASP A:335 , TYR A:383 , TYR A:466 , HOH A:771binding site for residue 3C5 A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y2P)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:16 -Pro A:17
2Lys A:160 -Pro A:161
3Phe A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y2P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y2P)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y2P)

(-) 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    
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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:546
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......ee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh...eeeehhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeee..hhhhhhhhhhhhhh..............hhhhheeeeeeee..eeeeeeee....eeeee.....hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhh................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.........eeeeee......hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y2p A   2 TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541      

   Legend:   → Mismatch (orange background)
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  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 4Y2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y2P)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HYES_HUMAN | P349131s8o 1vj5 1zd2 1zd3 1zd4 1zd5 3ans 3ant 3i1y 3i28 3koo 3otq 3pdc 3wk4 3wk5 3wk6 3wk7 3wk8 3wk9 3wka 3wkb 3wkc 3wkd 3wke 4c4x 4c4y 4c4z 4hai 4j03 4jnc 4ocz 4od0 4x6x 4x6y 4y2j 4y2q 4y2r 4y2s 4y2t 4y2u 4y2v 4y2x 4y2y 5ahx 5ai0 5ai4 5ai5 5ai6 5ai8 5ai9 5aia 5aib 5aic 5ak3 5ak4 5ak5 5ak6 5ake 5akg 5akh 5aki 5akj 5akk 5akl 5akx 5aky 5akz 5ald 5ale 5alf 5alg 5alh 5ali 5alj 5alk 5all 5alm 5aln 5alo 5alp 5alq 5alr 5als 5alt 5alu 5alv 5alw 5alx 5aly 5alz 5am0 5am1 5am2 5am3 5am4 5am5 5fp0

(-) Related Entries Specified in the PDB File

4y2j 4y2q 4y2r 4y2s 4y2t 4y2u 4y2v 4y2x 4y2y