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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 :  1.80
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
    Chains: A, B
    EC Number: 3.1.4.39
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Expression System Vector Type: BACMID
    Fragment: UNP RESIDUES 17-863
    Gene: ENPP2, ATX, PDNP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: E-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  (8, 32)

Asymmetric Unit (8, 32)
No.NameCountTypeFull Name
14NY2Ligand/Ion4-{(Z)-2-[6-CHLORO-1-(4-FLUOROBENZYL)-1H-INDOL-3-YL]-1-CYANOETHENYL}BENZOIC ACID
2BMA2Ligand/IonBETA-D-MANNOSE
3CA2Ligand/IonCALCIUM ION
4GOL2Ligand/IonGLYCEROL
5NA4Ligand/IonSODIUM ION
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN12Ligand/IonTHIOCYANATE ION
8ZN4Ligand/IonZINC ION
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
14NY1Ligand/Ion4-{(Z)-2-[6-CHLORO-1-(4-FLUOROBENZYL)-1H-INDOL-3-YL]-1-CYANOETHENYL}BENZOIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4GOL1Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN7Ligand/IonTHIOCYANATE ION
8ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
14NY1Ligand/Ion4-{(Z)-2-[6-CHLORO-1-(4-FLUOROBENZYL)-1H-INDOL-3-YL]-1-CYANOETHENYL}BENZOIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4GOL1Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN5Ligand/IonTHIOCYANATE ION
8ZN-1Ligand/IonZINC ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:172 , THR A:210 , ASP A:359 , HIS A:360binding site for residue ZN A 904
02AC2SOFTWAREASP A:312 , HIS A:316 , HIS A:475 , GOL A:909 , HOH A:1001binding site for residue ZN A 905
03AC3SOFTWAREASP A:740 , ASP A:742 , ASP A:744 , LEU A:746 , ASP A:748 , HOH A:1250binding site for residue CA A 906
04AC4SOFTWARETYR A:670 , ASP A:673 , MET A:676 , HOH A:1258binding site for residue NA A 907
05AC5SOFTWAREASN A:802 , SER A:805 , SER A:808 , HOH A:1185 , HOH A:1261 , HOH A:1266binding site for residue NA A 908
06AC6SOFTWARELYS A:209 , THR A:210 , ASN A:231 , ASP A:312 , HIS A:316 , HIS A:475 , ZN A:905 , HOH A:1022binding site for residue GOL A 909
07AC7SOFTWARESER A:170 , LEU A:214 , LEU A:217 , ALA A:218 , PHE A:274 , PHE A:275 , TRP A:276 , TYR A:307 , ASP A:359 , HOH A:1003binding site for residue 4NY A 910
08AC8SOFTWAREHIS A:282 , SER A:308binding site for residue SCN A 911
09AC9SOFTWAREPRO A:788 , LEU A:789 , ARG A:844 , GLU A:848 , HOH A:1182binding site for residue SCN A 912
10AD1SOFTWARELYS A:500binding site for residue SCN A 913
11AD2SOFTWARECYS A:157binding site for residue SCN A 914
12AD3SOFTWAREPRO A:207 , LYS A:209 , GLY A:230 , ASN A:231 , ARG A:392binding site for residue SCN A 915
13AD4SOFTWAREVAL A:448 , ARG A:450 , VAL A:481 , HOH A:1082binding site for residue SCN A 916
14AD5SOFTWAREHIS A:226 , GLY A:227 , ARG A:253 , TRP A:254 , GLY A:256 , ARG A:440binding site for residue SCN A 917
15AD6SOFTWAREASP B:172 , THR B:210 , ASP B:359 , HIS B:360binding site for residue ZN B 904
16AD7SOFTWAREASP B:312 , HIS B:316 , HIS B:475 , GOL B:909binding site for residue ZN B 905
17AD8SOFTWAREASN B:802 , SER B:805 , SER B:808 , HOH B:1187 , HOH B:1279 , HOH B:1283binding site for residue NA B 906
18AD9SOFTWAREASP B:740 , ASP B:742 , ASP B:744 , LEU B:746 , ASP B:748 , HOH B:1256binding site for residue CA B 907
19AE1SOFTWARETYR B:670 , ASP B:673 , MET B:676 , HOH B:1216 , HOH B:1262binding site for residue NA B 908
20AE2SOFTWARELYS B:209 , THR B:210 , ASN B:231 , ASP B:312 , HIS B:316 , HIS B:475 , ZN B:905 , HOH B:1266binding site for residue GOL B 909
21AE3SOFTWARESER B:170 , LEU B:214 , LEU B:217 , ALA B:218 , LEU B:244 , PHE B:274 , PHE B:275 , TRP B:276 , ALA B:305 , TYR B:307 , ASP B:359 , HOH B:1003binding site for residue 4NY B 910
22AE4SOFTWAREHIS B:282 , SER B:308 , ILE B:332 , ILE B:335 , HOH B:1067binding site for residue SCN B 911
23AE5SOFTWARELEU B:789 , HOH B:1002binding site for residue SCN B 912
24AE6SOFTWAREHIS B:226 , ARG B:253 , TRP B:254 , GLY B:256 , ARG B:440 , HOH B:1011 , HOH B:1259binding site for residue SCN B 913
25AE7SOFTWAREPRO B:207 , LYS B:209 , GLY B:230 , ASN B:231 , ARG B:392binding site for residue SCN B 914
26AE8SOFTWARECYS B:157binding site for residue SCN B 915
27AE9SOFTWARELEU A:221 , PRO A:523 , ASN A:525 , LEU A:746 , HIS A:832 , HOH A:1013 , HOH A:1027 , HOH A:1048 , HOH A:1051 , HOH A:1108 , HOH A:1150 , HOH A:1164binding site for Poly-Saccharide residues NAG A 901 through BMA A 903 bound to ASN A 525
28AF1SOFTWARELEU B:221 , PRO B:523 , ASN B:525 , LEU B:746 , HIS B:832 , HOH B:1006 , HOH B:1059 , HOH B:1065 , HOH B:1082 , HOH B:1113 , HOH B:1136 , HOH B:1169 , HOH B:1250binding site for Poly-Saccharide residues NAG B 901 through BMA B 903 bound to ASN B 525

(-) SS Bonds  (25, 25)

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:414 -A:806
12A:775 -A:785
13B:59 -B:76
14B:63 -B:94
15B:74 -B:87
16B:80 -B:86
17B:103 -B:120
18B:108 -B:138
19B:118 -B:131
20B:124 -B:130
21B:149 -B:195
22B:157 -B:351
23B:414 -B:806
24B:567 -B:667
25B: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 4ZG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZG6)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZG6)

(-) 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:754
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhh........hhhhh..............hhhhhh....hhhhhhhh..hhhhh..................eeeeee...hhhhhhhhhhhhhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhh........eeeee.hhhhhhhh.........eeeee....eee......ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh....hhhhh.....ee.....eeee.....eeeee....eeeeeeeee................hhhhh.hhhhhhhh...eeee..hhhhh...hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhh.............eeeeeeeee.............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zg6 A  57 GSCKGRCFELCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIAALTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQAEVSSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYE 860
                                    66|       83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453    || 474       484       494       504       514       524       534       544       554       564 ||    599       609       619       629       639   ||  656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856    
                                    66|                                                                                                                                                                                                                                                                                                                                                                                             458|                                                                                             566|                                                643|                                                                                                                                                                                                                 
                                     74                                                                                                                                                                                                                                                                                                                                                                                              470                                                                                              592                                                 651                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:756
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhh....hhhhhhh........hhhhh..............hhhhhh....hhhhhhhh..hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee......ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh.....hhhhhh.....ee.....eeeee....eeeee.....eeeeeeee................hhhhh..hhhhhhh...eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zg6 B  57 GSCKGRCFELCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIAALTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGCSTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQAEVSSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYE 860
                                    66|       83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453    || 474       484       494       504       514       524       534       544       554       564  ||   597       607       617       627       637     ||654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854      
                                    66|                                                                                                                                                                                                                                                                                                                                                                                             458|                                                                                              567|                                                 643|                                                                                                                                                                                                                 
                                     74                                                                                                                                                                                                                                                                                                                                                                                              470                                                                                               591                                                  651
   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 4ZG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZG6)

(-) Gene Ontology  (34, 34)

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  4zg6
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  ENPP2_HUMAN | Q13822
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  3.1.4.39
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENPP2_HUMAN | Q13822: 4zg7 4zg9 4zga 5kxa

(-) Related Entries Specified in the PDB File

4zg7 4zg9 4zga