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(-) Description

Title :  HUMAN DIPEPTIDYL PEPTIDASE IV/CD26 IN COMPLEX WITH THE LONG-ACTING INHIBITOR OMARIGLIPTIN (MK-3102)
 
Authors :  G. Scapin, Y. Yan
Date :  22 Feb 14  (Deposition) - 09 Apr 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta, Beta-Propeller, Dimer, Diabetes, Aminopeptidase, Cell Membrane, Disulfide Bond, Glycoprotein, Secreted, Serine Protease, Signal-Anchor, Transmembrane, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Biftu, R. Sinha-Roy, P. Chen, X. Qian, D. Feng, J. T. Kuethe, G. Scapin, Y. D. Gao, Y. Yan, D. Krueger, A. Bak, G. Eiermann, J. He, J. Cox, J. Hicks, K. Lyons, H. He, G. Salituro, S. Tong, S. Patel, G. Doss A. Petrov, J. Wu, S. S. Xu, C. Sewall, X. Zhang, B. Zhang, N. A. Thornberry, A. E. Weber
Omarigliptin (Mk-3102): A Novel Long-Acting Dpp-4 Inhibitor For Once-Weekly Treatment Of Type 2 Diabetes.
J. Med. Chem. V. 57 3205 2014
PubMed-ID: 24660890  |  Reference-DOI: 10.1021/JM401992E

(-) Compounds

Molecule 1 - DIPEPTIDYL PEPTIDASE 4
    Chains: A, B
    EC Number: 3.4.14.5
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PBLUEBAC4.5
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 39-766)
    Gene: ADCP2, CD26, DPP4
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADABP, ADENOSINE DEAMINASE COMPLEXING PROTEIN 2, ADCP-2, DIPEPTIDYL PEPTIDASE IV, DPP IV, T-CELL ACTIVATION ANTIGEN CD26, TP103, DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM, DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
12VH2Ligand/Ion(2R,3S,5R)-5-[2-(METHYLSULFONYL)-2,6-DIHYDROPYRROLO[3,4-C]PYRAZOL-5(4H)-YL]-2-(2,4,5-TRIFLUOROPHENYL)TETRAHYDRO-2H-PYRAN-3-AMINE
2NA1Ligand/IonSODIUM ION
3NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:490 , LEU A:491 , LEU B:276 , VAL B:279 , HOH B:979BINDING SITE FOR RESIDUE NA A 801
02AC2SOFTWAREARG A:125 , GLU A:205 , GLU A:206 , PHE A:357 , TYR A:547 , SER A:630 , TYR A:631 , VAL A:656 , TYR A:662 , TYR A:666 , ASN A:710 , VAL A:711 , HIS A:740 , HOH A:935 , HOH A:1108 , HOH A:1184 , HOH A:1323BINDING SITE FOR RESIDUE 2VH A 802
03AC3SOFTWAREARG B:125 , GLU B:205 , GLU B:206 , PHE B:357 , TYR B:547 , SER B:630 , TYR B:631 , VAL B:656 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711 , HIS B:740 , HOH B:985 , HOH B:990 , HOH B:1527BINDING SITE FOR RESIDUE 2VH B 801
04AC4SOFTWAREGLU A:67 , VAL A:78 , ASN A:85 , SER A:86 , SER A:87 , HOH A:1516 , HOH A:1688 , HOH A:1692BINDING SITE FOR MONO-SACCHARIDE NAG A 803 BOUND TO ASN A 85
05AC5SOFTWAREILE A:148 , ASN A:150 , HOH A:1428 , HOH A:1628BINDING SITE FOR MONO-SACCHARIDE NAG A 804 BOUND TO ASN A 150
06AC6SOFTWAREASN A:219 , THR A:221 , GLN A:308 , GLU A:309 , TYR A:330 , GLU A:332 , HOH A:1573BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 219 RESIDUES 805 TO 806
07AC7SOFTWAREILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , HOH A:1269 , HOH A:1316 , HOH A:1411BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 229 RESIDUES 807 TO 808
08AC8SOFTWARETRP A:187 , VAL A:279 , ASN A:281BINDING SITE FOR MONO-SACCHARIDE NAG A 809 BOUND TO ASN A 281
09AC9SOFTWAREILE A:319 , ASN A:321 , SER A:349 , THR A:350 , ARG A:596 , HOH A:1676BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 321 RESIDUES 810 TO 811
10BC1SOFTWAREGLU B:67 , VAL B:78 , ASN B:85 , SER B:86 , SER B:87 , HOH B:1376 , HOH B:1402 , HOH B:1684 , HOH B:1699BINDING SITE FOR MONO-SACCHARIDE NAG B 802 BOUND TO ASN B 85
11BC2SOFTWAREGLU B:73 , ASN B:74 , ASN B:75 , ASN B:92BINDING SITE FOR MONO-SACCHARIDE NAG B 803 BOUND TO ASN B 92
12BC3SOFTWAREARG B:147 , ILE B:148 , ASN B:150 , HOH B:1313BINDING SITE FOR MONO-SACCHARIDE NAG B 804 BOUND TO ASN B 150
13BC4SOFTWAREASN B:219 , THR B:221 , PHE B:222 , ASN B:272 , GLN B:308 , GLU B:309 , TYR B:330 , GLU B:332 , HOH B:1258 , HOH B:1309 , HOH B:1327 , HOH B:1519 , HOH B:1548 , HOH B:1608BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 219 RESIDUES 805 TO 806
14BC5SOFTWAREILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , HOH B:1196 , HOH B:1416 , HOH B:1610BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 229 RESIDUES 807 TO 808
15BC6SOFTWAREASN A:450 , TRP B:187 , ASN B:281 , HOH B:1230 , HOH B:1639 , HOH B:1687 , HOH B:1694 , HOH B:1695 , HOH B:1696 , HOH B:1697 , HOH B:1704BINDING SITE FOR MONO-SACCHARIDE NAG B 809 BOUND TO ASN B 281
16BC7SOFTWAREASN B:321 , SER B:349 , HOH B:1497 , HOH B:1585BINDING SITE FOR MONO-SACCHARIDE NAG B 810 BOUND TO ASN B 321

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:328 -A:339
2A:385 -A:394
3A:444 -A:447
4A:454 -A:472
5A:649 -A:762
6B:328 -B:339
7B:385 -B:394
8B:444 -B:447
9B:454 -B:472
10B:649 -B:762

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:474 -Pro A:475
2Gly B:474 -Pro B:475

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PNZ)

(-) 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:728
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4pnza1 A:39-508 Dipeptidyl peptidase IV/CD26, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                      d4pnza2 A:509-766 Dipeptidyl peptidase IV/CD26, C-terminal domain                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhh..........ee....eeeeee..eeeeee.....eeeee...........eeeeee.....eeeeeeeeee.....eeeeeeeee....ee...........eeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee...........eeee..hhhhhh..eeeeeeeeee..eeeeeeee....eeeeeeeeee....eeee.hhhheeee..............ee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee......eee.........eeeeeeee.....eeeeeeeee...eeeeee....eeeeeee.hhhhhhhhh.ee..eeeeeeeee..eeeeeeeee.........eeeeeee...............hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pnz A  39 TRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 766
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758        


Chain B from PDB  Type:PROTEIN  Length:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4pnzb1 B:40-508 Dipeptidyl peptidase IV/CD26, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                     d4pnzb2 B:509-766 Dipeptidyl peptidase IV/CD26, C-terminal domain                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhh.........ee....eeeeee..eeeeee.....eeeee...........eeeeee.....eeeeeeeeee.....eeeeeeeee....ee.........eeeeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee.hhh.......eeee..hhhhhh..eeeeeeeeee..eeeeeeee....eeeeeeeeee....eeee.hhhheeee..............ee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee..eeeeeee............eeeee.....eeeeee......eeeeee....eeeeeee.hhhhhhhhh.ee..eeeeeeeee..eeeeeeeee.........eeeeeee...............hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pnz B  40 RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 766
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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
        DPP4_HUMAN | P27487: 1j2e 1n1m 1nu6 1nu8 1pfq 1r9m 1r9n 1rwq 1tk3 1tkr 1u8e 1w1i 1wcy 1x70 2ajl 2bgn 2bgr 2bub 2fjp 2g5p 2g5t 2g63 2hha 2i03 2i78 2iit 2iiv 2jid 2oag 2ogz 2ole 2onc 2oph 2oqi 2oqv 2p8s 2qjr 2qky 2qoe 2qt9 2qtb 2rgu 2rip 3bjm 3c43 3c45 3ccb 3ccc 3d4l 3eio 3f8s 3g0b 3g0c 3g0d 3g0g 3h0c 3hab 3hac 3kwf 3kwj 3nox 3o95 3o9v 3oc0 3opm 3q0t 3q8w 3qbj 3sww 3sx4 3vjk 3vjl 3vjm 3w2t 3wqh 4a5s 4dsa 4dsz 4dtc 4g1f 4j3j 4jh0 4kr0 4l72 4lko 4n8d 4n8e 4pv7 4qzv 5i7u 5ism 5j3j 5kby 5t4b 5t4e 5t4f 5t4h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PNZ)