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(-) Description

Title :  STRUCTURAL BASIS FOR INHIBITION OF HUMAN AUTOTAXIN BY FOUR NOVEL COMPOUNDS
 
Authors :  A. J. Stein, G. Bain, J. H. Hutchinson, J. F. Evans
Date :  22 Apr 15  (Deposition) - 14 Oct 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Autotaxin, Enpp2, Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Stein, G. Bain, P. Prodanovich, A. M. Santini, J. Darlington, N. M. Stelzer, R. S. Sidhu, J. Schaub, L. Goulet, D. Lonergan, I. Calderon, J. F. Evans, J. H. Hutchinson
Structural Basis For Inhibition Of Human Autotaxin By Four Potent Compounds With Distinct Modes Of Binding.
Mol. Pharmacol. V. 88 982 2015
PubMed-ID: 26371182  |  Reference-DOI: 10.1124/MOL.115.100404

(-) Compounds

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
    ChainsA
    EC Number3.1.4.39
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    Expression System Vector TypeBACMID
    GeneENPP2, ATX, PDNP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
14O31Ligand/Ion(11AS)-6-(4-FLUOROBENZYL)-5,6,11,11A-TETRAHYDRO-1H-IMIDAZO[1',5':1,6]PYRIDO[3,4-B]INDOLE-1,3(2H)-DIONE
2ACD1Ligand/IonARACHIDONIC ACID
3CA2Ligand/IonCALCIUM ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SCN2Ligand/IonTHIOCYANATE ION
7ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:312 , HIS A:316 , HIS A:475 , EDO A:905binding site for residue ZN A 903
2AC2SOFTWAREASP A:740 , ASP A:742 , ASP A:744 , LEU A:746 , ASP A:748binding site for residue CA A 904
3AC3SOFTWAREASP A:172 , THR A:210 , ASN A:231 , ASP A:312 , HIS A:316 , HIS A:475 , ZN A:903 , HOH A:1009binding site for residue EDO A 905
4AC4SOFTWARESER A:308binding site for residue SCN A 906
5AC5SOFTWARELEU A:789 , ARG A:844 , GLU A:848binding site for residue SCN A 907
6AC6SOFTWARETYR A:670 , ASP A:673 , MET A:676binding site for residue CA A 908
7AC7SOFTWARESER A:82 , LYS A:249 , PHE A:250binding site for residue ACD A 909
8AC8SOFTWAREILE A:168 , PHE A:211 , LEU A:214 , TYR A:215 , PHE A:274 , PHE A:275 , TRP A:276 , TYR A:307binding site for residue 4O3 A 910
9AC9SOFTWARELEU A:221 , PRO A:523 , ASN A:525 , ASP A:744binding site for Poly-Saccharide residues NAG A 901 through NAG A 902 bound to ASN A 525

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:76
2A:63 -A:94
3A:74 -A:87
4A:80 -A:86
5A:103 -A:120
6A:108 -A:138
7A:118 -A:131
8A:124 -A:130
9A:149 -A:195
10A:157 -A:351
11A:414 -A:806
12A:775 -A:785

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:206 -Pro A:207
2Gln A:310 -Pro A:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZGA)

(-) 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:740
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhh....hhhhhhh........hhhhh..........hhhhhh....hhhhhhhh..hhhhh..................eeeeeee..hhhhhhhh...hhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....ee......ee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhh.........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh......eeee....eeeee...hhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee......ee......hhhhh..eeee.......ee...ee..hhhhhhhhh..............hhhhh.......................hhhhh....hhhhh.....ee.....eeeee....eeeee....eeeeeeeee............hhhhh.hhhhhhh....eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.............eeeeeeeee.............hhhhhhhhhhhhh..hhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zga A  57 GSCKGRCFELCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGNEENACHCEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFDPKAIIANLTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQACVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYE 860
                                    66|       83        93       103     ||116   ||  127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397|      413       423       433       443       453    || 474       484       494       504       514       524       534       544       554       564 ||    599       609       619       629       639||     660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860
                                    66|                                109|    120|                                                                                                                                                                                                                                                                                397|                                                   458|                                                                                             566|                                             640|                                                                                                                                                                                                                
                                     74                                 113     122                                                                                                                                                                                                                                                                                 404                                                    470                                                                                              592                                              652                                                                                                                                                                                                                

   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 4ZGA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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
        ENPP2_HUMAN | Q138224zg6 4zg7 4zg9 5kxa

(-) Related Entries Specified in the PDB File

4zg6 4zg7 4zg9