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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 :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  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  (7, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
14O24Ligand/Ion3-[(11AS)-6-(4-FLUOROBENZYL)-1,3-DIOXO-5,6,11,11A-TETRAHYDRO-1H-IMIDAZO[1',5':1,6]PYRIDO[3,4-B]INDOL-2(3H)-YL]PROPANOIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA2Ligand/IonCALCIUM ION
4EDO3Ligand/Ion1,2-ETHANEDIOL
5NA4Ligand/IonSODIUM ION
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
14O22Ligand/Ion3-[(11AS)-6-(4-FLUOROBENZYL)-1,3-DIOXO-5,6,11,11A-TETRAHYDRO-1H-IMIDAZO[1',5':1,6]PYRIDO[3,4-B]INDOL-2(3H)-YL]PROPANOIC ACID
2BMA-1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4EDO2Ligand/Ion1,2-ETHANEDIOL
5NA-1Ligand/IonSODIUM ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
14O22Ligand/Ion3-[(11AS)-6-(4-FLUOROBENZYL)-1,3-DIOXO-5,6,11,11A-TETRAHYDRO-1H-IMIDAZO[1',5':1,6]PYRIDO[3,4-B]INDOL-2(3H)-YL]PROPANOIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5NA-1Ligand/IonSODIUM ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:312 , HIS A:316 , HIS A:475 , EDO A:910binding site for residue ZN A 903
02AC2SOFTWAREASP A:172 , THR A:210 , ASP A:359 , HIS A:360binding site for residue ZN A 904
03AC3SOFTWAREASP A:740 , ASP A:742 , ASP A:744 , LEU A:746 , ASP A:748binding site for residue CA A 905
04AC4SOFTWARETYR A:670 , ASP A:673 , MET A:676 , HOH A:1018binding site for residue NA A 906
05AC5SOFTWAREASN A:802 , SER A:805 , SER A:808 , HOH A:1004 , HOH A:1006 , SER B:466binding site for residue NA A 907
06AC6SOFTWAREILE A:168 , SER A:170 , LEU A:214 , TYR A:215 , PHE A:274 , PHE A:275 , TRP A:276 , ARG A:285 , TYR A:307binding site for residue 4O2 A 908
07AC7SOFTWAREASP A:235 , PHE A:242 , TRP A:254 , TRP A:255 , ARG A:440 , ASP B:235 , PHE B:238 , TRP B:254 , ARG B:439 , ARG B:440 , 4O2 B:910binding site for residue 4O2 A 909
08AC8SOFTWARETHR A:210 , ASN A:231 , HIS A:475 , ZN A:903 , HOH A:1003binding site for residue EDO A 910
09AC9SOFTWAREPHE A:709 , PRO A:797 , ARG A:799 , ASN A:802 , HOH A:1013binding site for residue EDO A 911
10AD1SOFTWAREASP B:312 , HIS B:316 , HIS B:475 , EDO B:911binding site for residue ZN B 904
11AD2SOFTWAREASP B:172 , THR B:210 , ASP B:359 , HIS B:360binding site for residue ZN B 905
12AD3SOFTWAREASP B:740 , ASP B:742 , ASP B:744 , LEU B:746 , ASP B:748 , HOH B:1001binding site for residue CA B 906
13AD4SOFTWARETYR B:670 , ASP B:673 , MET B:676 , HOH B:1006binding site for residue NA B 907
14AD5SOFTWAREASN B:802 , SER B:805 , SER B:808 , HOH B:1008binding site for residue NA B 908
15AD6SOFTWARESER B:170 , LEU B:214 , TYR B:215 , ARG B:247 , PHE B:274 , PHE B:275 , TRP B:276 , VAL B:278 , ARG B:285 , TYR B:307binding site for residue 4O2 B 909
16AD7SOFTWAREPHE A:238 , PHE A:242 , 4O2 A:909 , MET B:233 , PHE B:242 , LYS B:249 , TRP B:254 , TRP B:255 , ARG B:440binding site for residue 4O2 B 910
17AD8SOFTWARELYS B:209 , THR B:210 , ASN B:231 , HIS B:316 , HIS B:475 , ZN B:904binding site for residue EDO B 911
18AD9SOFTWARELEU A:221 , PRO A:523 , ASN A:525 , HIS A:832binding site for Poly-Saccharide residues NAG A 901 through NAG A 902 bound to ASN A 525
19AE1SOFTWAREPRO B:523 , ASN B:525 , HIS B:832binding site for Poly-Saccharide residues NAG B 901 through BMA B 903 bound to ASN B 525

(-) SS Bonds  (27, 27)

Asymmetric 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:367 -A:469
12A:414 -A:806
13A:775 -A:785
14B:59 -B:76
15B:63 -B:94
16B:74 -B:87
17B:80 -B:86
18B:103 -B:120
19B:108 -B:138
20B:118 -B:131
21B:124 -B:130
22B:149 -B:195
23B:157 -B:351
24B:367 -B:469
25B:414 -B:806
26B:567 -B:667
27B:775 -B:785

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:206 -Pro A:207
2Gln A:310 -Pro A:311
3Tyr B:206 -Pro B:207
4Gln B:310 -Pro B:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZG9)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZG9)

(-) 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:750
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhh....hhhhhh............................hhhhhh....hhhhhhh..........................eeeeee...hhhhhh.....hhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh....eeee....eeee..hhhhh...hhhhhhhhh.............hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.......ee.............eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh..................eeeee....eeeee....eeeeeeeee.................hhhhh.hhhhhhh....eeee..hhhhh....hhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhh.........hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zg9 A  58 SCKGRCFELQPDCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIANLTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPCFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGRHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQPDHLTSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYE 860
                                    67|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  ||   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456 ||    476       486       496       506       516       526       536       546       556       566|      604       614       624       634    || 650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860
                                    67|                                                                                                                                                                         244|                                                                                                                                                                                                             458|                                                                                              566|                                         639|                                                                                                                                                                                                                      
                                     72                                                                                                                                                                          250                                                                                                                                                                                                              469                                                                                               595                                          646                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:764
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhh....hhhhhhh........hhhhh......................hhhhhh....hhhhh..................eeeeee...hhhhhh.....hhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh....eeee....eeee.......hhhhh...hhhhhhhhh.............hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.................ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh.....hhhhhh.....ee.....eeee.....eeeee.....eeeeeeee...........hhhhh.hhhhhhhh...eeee..hhhhh..hhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhh.............eeeeeeeee.............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zg9 B  58 SCKGRCFELQEADCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLADCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIANLTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGCSTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYES 861
                                    67 ||     80        90       100       110       120     ||132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562    || 595       605       615       625       635   ||  657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857    
                                      69|                                                  126|                                                                                                                                                                                                                                                                                                                                                                                                                                                   567|                                             639|                                                                                                                                                                                                                 
                                       73                                                   129                                                                                                                                                                                                                                                                                                                                                                                                                                                    591                                              652                                                                                                                                                                                                                 

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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 4ZG9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZG9)

(-) Gene Ontology  (34, 34)

Asymmetric 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 4zga 5kxa

(-) Related Entries Specified in the PDB File

4zg6 4zg7 4zga