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(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOTAXIN AND COMPOUND 1
 
Authors :  J. D. Durbin
Date :  27 Jul 16  (Deposition) - 10 Aug 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phospholipase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Jones, L. A. Pfeifer, T. J. Bleisch, T. J. Beauchamp, J. D. Durbin, V. J. Klimkowski, N. E. Hughes, C. J. Rito, Y. Dao, J. M. Gruber, H. Bui, M. G. Chambers, S. Chandrasekhar, C. Lin, D. J. Mccann, D. R. Mudra, J. L. Oskins, C. A. Swearingen, K. Thirunavukkarasu, B. H. Norman
Novel Autotaxin Inhibitors For The Treatment Of Osteoarthritis Pain: Lead Optimization Via Structure-Based Drug Design.
Acs Med. Chem. Lett. V. 7 857 2016
PubMed-ID: 27660691  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00207

(-) Compounds

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
    Chains: A, B
    EC Number: 3.1.4.39
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: ENPP2, ATX, NPPS2
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    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  (6, 27)

Asymmetric Unit (6, 27)
No.NameCountTypeFull Name
16ZN2Ligand/Ion6-(3-{2-[(2,3-DIHYDRO-1H-INDEN-2-YL)AMINO]-7,8-DIHYDROPYRIDO[4,3-D]PYRIMIDIN-6(5H)-YL}PROPANOYL)-1,3-BENZOXAZOL-2(3H)-ONE
2BMA2Ligand/IonBETA-D-MANNOSE
3CL2Ligand/IonCHLORIDE ION
4MAN9Ligand/IonALPHA-D-MANNOSE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN6Ligand/IonZINC ION
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
16ZN1Ligand/Ion6-(3-{2-[(2,3-DIHYDRO-1H-INDEN-2-YL)AMINO]-7,8-DIHYDROPYRIDO[4,3-D]PYRIMIDIN-6(5H)-YL}PROPANOYL)-1,3-BENZOXAZOL-2(3H)-ONE
2BMA1Ligand/IonBETA-D-MANNOSE
3CL-1Ligand/IonCHLORIDE ION
4MAN6Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
16ZN1Ligand/Ion6-(3-{2-[(2,3-DIHYDRO-1H-INDEN-2-YL)AMINO]-7,8-DIHYDROPYRIDO[4,3-D]PYRIMIDIN-6(5H)-YL}PROPANOYL)-1,3-BENZOXAZOL-2(3H)-ONE
2BMA1Ligand/IonBETA-D-MANNOSE
3CL-1Ligand/IonCHLORIDE ION
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:169 , ASP A:171 , THR A:209 , LEU A:213 , LEU A:243 , PHE A:273 , PHE A:274 , TRP A:275 , TYR A:306 , ASP A:311 , PHE A:312 , HIS A:315 , HIS A:474 , ZN A:914binding site for residue 6ZN A 911
02AC2SOFTWAREASN A:230 , SER A:231 , ARG A:391binding site for residue CL A 912
03AC3SOFTWAREASP A:171 , THR A:209 , ASP A:358 , HIS A:359binding site for residue ZN A 913
04AC4SOFTWAREASP A:311 , HIS A:315 , HIS A:474 , 6ZN A:911binding site for residue ZN A 914
05AC5SOFTWAREASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747binding site for residue ZN A 915
06AC6SOFTWARESER B:169 , LEU B:213 , LEU B:216 , LEU B:243 , PHE B:273 , PHE B:274 , TRP B:275 , TYR B:306 , ASP B:311 , PHE B:312 , HIS B:315 , HIS B:474 , ZN B:909binding site for residue 6ZN B 908
07AC7SOFTWAREASP B:311 , HIS B:315 , HIS B:474 , 6ZN B:908binding site for residue ZN B 909
08AC8SOFTWAREASP B:171 , THR B:209 , ASP B:358 , HIS B:359binding site for residue ZN B 910
09AC9SOFTWAREASP B:739 , ASN B:741 , ASP B:743 , LEU B:745 , ASP B:747binding site for residue ZN B 911
10AD1SOFTWAREASN B:230 , ARG B:391binding site for residue CL B 912
11AD2SOFTWARELEU A:376 , THR A:377 , ASN A:378 , THR A:406 , ASN A:410 , HOH A:1002binding site for Mono-Saccharide NAG A 910 bound to ASN A 410
12AD3SOFTWAREGLU A:223 , SER A:224 , GLY A:255 , GLY A:256 , GLN A:257 , LYS A:265 , ASN A:436 , ASN A:437 , PRO A:522 , ASN A:524 , LEU A:745 , HIS A:831 , HOH A:1016 , ASP B:750 , LYS B:753binding site for Poly-Saccharide residues NAG A 901 through MAN A 909 bound to ASN A 524
13AD4SOFTWARELEU B:376 , THR B:377 , THR B:406 , ASN B:410 , HOH B:1027binding site for Mono-Saccharide NAG B 907 bound to ASN B 410
14AD5SOFTWAREGLU B:223 , SER B:224 , GLY B:255 , ASN B:436 , ASN B:437 , PRO B:522 , ASN B:524 , LEU B:745 , HIS B:831 , HOH B:1018 , HOH B:1024binding site for Poly-Saccharide residues NAG B 901 through MAN B 906 bound to ASN B 524

(-) SS Bonds  (30, 30)

Asymmetric Unit
No.Residues
1A:58 -A:75
2A:62 -A:93
3A:73 -A:86
4A:79 -A:85
5A:102 -A:119
6A:107 -A:137
7A:117 -A:130
8A:123 -A:129
9A:148 -A:194
10A:156 -A:350
11A:366 -A:468
12A:413 -A:805
13A:566 -A:666
14A:568 -A:651
15A:774 -A:784
16B:58 -B:75
17B:62 -B:93
18B:73 -B:86
19B:79 -B:85
20B:102 -B:119
21B:107 -B:137
22B:117 -B:130
23B:123 -B:129
24B:148 -B:194
25B:156 -B:350
26B:366 -B:468
27B:413 -B:805
28B:566 -B:666
29B:568 -B:651
30B:774 -B:784

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:70 -Pro A:71
2Tyr A:205 -Pro A:206
3Gln A:309 -Pro A:310
4Pro B:70 -Pro B:71
5Tyr B:205 -Pro B:206
6Gln B:309 -Pro B:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L0E)

(-) Exons   (0, 0)

(no "Exon" information available for 5L0E)

(-) 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:783
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhh.......hhhhhhh........hhhhh..............hhhhhh....hhhhhh....hhhhh..................eeeeeee....hhhhhhhhhhhhhhhhhhhheeeeeee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhh.......hhhhhhhh..............hhhhhhhhhhhhh.........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.........ee......hhhhheeeeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh..........hhhhhhh.....ee.....eeeee....eeeee.....eeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh...hhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l0e A  52 TNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDKGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    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       469       479       489       499       509       519       529       539       549       559       569 ||    596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856   
                                                                                                                                                                                                                                                                                                                                                                                                                                                 459|                                                                                                    571|                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                  468                                                                                                     589                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:782
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhh.......hhhhhhh........hhhhh..............hhhhhh....hhhhhh....hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhheeeeeee.....hhhhhhhhhhhh.hhhhhh.....eee....eee................hhhhhhhh..............hhhhhhhhhhhhh.........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee...........eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.................hhhhheeeeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh.........hhhhhhh.....ee.....eeeee....eeeee....eeeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh...hhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l0e B  52 TNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    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       469       479       489       499       509       519       529       539       549       559       569||     597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857  
                                                                                                                                                                                                                                                                                                                                                                                                                                                 459|                                                                                                   570|                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                  468                                                                                                    589
   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 5L0E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L0E)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)

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  5l0e
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  ENPP2_RAT | Q64610
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  3.1.4.39
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 Related Entries

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

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        ENPP2_RAT | Q64610: 2xr9 2xrg 5dlt 5dlv 5dlw 5ijq 5ijs 5l0b 5l0k 5lqq

(-) Related Entries Specified in the PDB File

5l0b 5l0k