4N8D - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DPP4 COMPLEXED WITH SYN-7AA

Authors :   N. Ostermann, F. Zink, M. Kroemer

Date :   17 Oct 13 (Deposition) - 12 Feb 14 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Namoto, F. Sirockin, N. Ostermann, F. Gessier, S. Flohr, R. Sedrani B. Gerhartz, J. Trappe, U. Hassiepen, A. Duttaroy, S. Ferreira, J. M. Sutton, D. E. Clark, G. Fenton, M. Beswick, D. K. Baeschlin
Discovery Of C-(1-Aryl-Cyclohexyl)-Methylamines As Selective, Orally Available Inhibitors Of Dipeptidyl Peptidase Iv.
Bioorg. Med. Chem. Lett. V. 24 731 2014
PubMed-ID: 24439847 | Reference-DOI: 10.1016/J.BMCL.2013.12.118

Molecule 1 - DIPEPTIDYL PEPTIDASE 4
	Chains	:	A, B
	EC Number	:	3.4.14.5
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Fragment	:	UNP RESIDUES 39-766
	Gene	:	DPP4, ADCP2, CD26
	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 MEMBRANE FORM, DIPEPTIDYL PEPTIDASE IV MEMBRANE FORM, DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM, DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 25)

No.	Name	Count	Type	Full Name
1	2KS	2	Ligand/Ion	1-(CIS-1-PHENYL-4-{[(2E)-3-PHENYLPROP-2-EN-1-YL]OXY}CYCLOHEXYL)METHANAMINE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	14	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:596 , ARG A:597 , ASN A:679 , HOH A:1803 , HOH A:1814	BINDING SITE FOR RESIDUE SO4 A 812
02	AC2	SOFTWARE	GLU A:146 , ARG A:147 , HOH A:1412	BINDING SITE FOR RESIDUE SO4 A 813
03	AC3	SOFTWARE	ARG A:658 , ARG A:684 , HOH A:1075 , GLU B:244 , SER B:245	BINDING SITE FOR RESIDUE SO4 A 814
04	AC4	SOFTWARE	ARG A:125 , GLU A:205 , GLU A:206 , SER A:209 , ARG A:358 , SER A:630 , TYR A:662 , TYR A:666 , VAL A:711 , HIS A:740 , HOH A:1462	BINDING SITE FOR RESIDUE 2KS A 815
05	AC5	SOFTWARE	THR B:144 , GLU B:145 , GLU B:146 , ARG B:147 , HOH B:1657	BINDING SITE FOR RESIDUE SO4 B 807
06	AC6	SOFTWARE	ARG B:596 , ARG B:597 , ASP B:678 , ASN B:679	BINDING SITE FOR RESIDUE SO4 B 808
07	AC7	SOFTWARE	GLU A:244 , ARG B:658 , ARG B:684 , HOH B:1335 , HOH B:1654	BINDING SITE FOR RESIDUE SO4 B 809
08	AC8	SOFTWARE	ARG B:125 , GLU B:205 , GLU B:206 , SER B:209 , ARG B:358 , TYR B:547 , SER B:630 , TYR B:662 , TYR B:666 , VAL B:711 , HIS B:740 , HOH B:1346	BINDING SITE FOR RESIDUE 2KS B 810
09	AC9	SOFTWARE	GLU A:67 , VAL A:78 , ASN A:85 , SER A:86 , SER A:87 , LEU A:519 , ASN A:520 , GLU A:608 , ARG A:611 , NAG A:811 , HOH A:1071 , HOH A:1167 , HOH A:1184 , HOH A:1249 , HOH A:1279 , HOH A:1280 , HOH A:1443 , HOH A:1473 , HOH A:1664 , HOH A:1676 , HOH A:1710 , HOH A:1784 , HOH A:1812 , HOH A:1828 , HOH A:1830 , ASP B:393	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 85 RESIDUES 801 TO 805
10	BC1	SOFTWARE	ARG A:147 , ILE A:148 , ASN A:150 , HOH A:1345 , HOH A:1692	BINDING SITE FOR MONO-SACCHARIDE NAG A 806 BOUND TO ASN A 150
11	BC2	SOFTWARE	ASN A:219 , THR A:221 , GLN A:308 , GLU A:309 , HOH A:1519 , HOH A:1593	BINDING SITE FOR MONO-SACCHARIDE NAG A 807 BOUND TO ASN A 219
12	BC3	SOFTWARE	ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , HOH A:1147 , HOH A:1336 , HOH A:1790	BINDING SITE FOR MONO-SACCHARIDE NAG A 808 BOUND TO ASN A 229
13	BC4	SOFTWARE	TRP A:187 , VAL A:279 , ASN A:281 , HOH A:1202 , HOH A:1470	BINDING SITE FOR MONO-SACCHARIDE NAG A 809 BOUND TO ASN A 281
14	BC5	SOFTWARE	ASN A:321 , MET A:348 , SER A:349 , THR A:350 , HOH A:1364 , HOH A:1910 , HOH B:1605	BINDING SITE FOR MONO-SACCHARIDE NAG A 810 BOUND TO ASN A 321
15	BC6	SOFTWARE	ASN A:520 , ARG A:581 , ASP A:605 , MAN A:805	BINDING SITE FOR MONO-SACCHARIDE NAG A 811 BOUND TO ASN A 520
16	BC7	SOFTWARE	VAL B:78 , ASN B:85 , SER B:86 , SER B:87 , HOH B:1357	BINDING SITE FOR MONO-SACCHARIDE NAG B 801 BOUND TO ASN B 85
17	BC8	SOFTWARE	ARG B:147 , ILE B:148 , ASN B:150 , HOH B:1275 , HOH B:1315 , HOH B:1451	BINDING SITE FOR MONO-SACCHARIDE NAG B 802 BOUND TO ASN B 150
18	BC9	SOFTWARE	ASN B:219 , THR B:221 , GLN B:308 , GLU B:309 , HOH B:1220 , HOH B:1480	BINDING SITE FOR MONO-SACCHARIDE NAG B 803 BOUND TO ASN B 219
19	CC1	SOFTWARE	ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , HOH B:1096 , HOH B:1197 , HOH B:1236 , HOH B:1761	BINDING SITE FOR MONO-SACCHARIDE NAG B 804 BOUND TO ASN B 229
20	CC2	SOFTWARE	TRP B:187 , VAL B:279 , ASN B:281 , HOH B:1337 , HOH B:1498	BINDING SITE FOR MONO-SACCHARIDE NAG B 805 BOUND TO ASN B 281
21	CC3	SOFTWARE	ASN B:321 , MET B:348 , SER B:349 , THR B:350 , HOH B:1620 , HOH B:1698	BINDING SITE FOR MONO-SACCHARIDE NAG B 806 BOUND TO ASN B 321

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:474	-	Pro A:475
2	Gly B:474	-	Pro B:475

(no "SAP(SNP)/Variant" information available for 4N8D)

(no "PROSITE Motif" information available for 4N8D)

(no "Exon" information available for 4N8D)

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:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4n8da1 A:40-508 Dipeptidyl peptidase IV/CD26, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                     d4n8da2 A:509-766 automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhh........eee....eeeeee..eeeeee.....eeeee.............eeee.....eeeeeeeeee.....eeeeeeeee....ee...........eeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee.hhh........eee..hhhhhh..eeeeeeeeee..eeeeeeee....eeeeeeeee......eee.hhhheeee..............ee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee..eeeeeee............eeeee.....eeeeee......eeeeee....eeeeeee.hhhhhhhhh.ee..eeeeeeeee..eeeeeeeee.........eeeeee................hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8d A  40 RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLIDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 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

Chain B from PDB  Type:PROTEIN  Length:733
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4n8db1 B:40-508 Dipeptidyl peptidase IV/CD26, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                     d4n8db2 B:509-772 automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhh........eee....eeeeee..eeeeee.....eeeeehhhhhhh......eeee.....eeeeeeeeee.....eeeeeeeee....eee..........eeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee.hhh........eee..hhhhhh..eeeeeeeeee..eeeeeeee....eeeeeeeee......eee.hhhheeee..............ee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee..eeeeeee............eeeee.....eeeeee......eeeeee....eeeeeee.hhhhhhhhh.ee..eeeeeeeee..eeeeeeeee.........eeeeee................hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n8d B  40 RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLIDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLPAAASWS 772
                                    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       769

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: 8-bladed beta-propeller (135)

Superfamily: DPP6 N-terminal domain-like (99)

Family: DPP6 N-terminal domain-like (99)

Protein domain: Dipeptidyl peptidase IV/CD26, N-terminal domain (88)

Human (Homo sapiens) [TaxId: 9606] (80)

1a	d4n8da1	A:40-508
1b	d4n8db1	B:40-508

Class: Alpha and beta proteins (a/b) (23833)

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: automated matches (184)

Protein domain: automated matches (184)

Human (Homo sapiens) [TaxId: 9606] (42)

2a	d4n8da2	A:509-766
2b	d4n8db2	B:509-772

(no "CATH Domain" information available for 4N8D)

(no "Pfam Domain" information available for 4N8D)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:474 - Pro A:475	[ RasMol ]
		Gly B:474 - Pro B:475	[ RasMol ]

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	4n8d
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	DPP4_HUMAN \| P27487
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 25)

Sites (21, 21)

SS Bonds (10, 10)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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