Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T66252 | Target Info | |||
| Target Name | Dipeptidyl peptidase 9 (DPP-9) | ||||
| Synonyms | Dipeptidyl peptidase-like protein 9; Dipeptidyl peptidase IX; Dipeptidyl peptidase IV-related protein 2; DPRP2; DPRP-2; DPP IX; DPLP9; DP9 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | DPP9 | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 1G244 | Ligand Info | |||||
| Structure Description | DPP9 - 1G244 | PDB:6EOR | ||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [1] |
| PDB Sequence |
AARFQVQKHS
30 WDGLRSIIHG40 SRKAPHDFQF58 VQKSGPHSHR71 LYYLGMPYRE83 NSLLYSEIPK 93 LLLSWKQMLD110 HFQATPHHGV120 YSREEELLRE130 RKRLGVFGIT140 SYDFHSESGL 150 FLFQASNSLF160 HCRDGGKNGF170 MVSPMKPLEI180 KTQCSGPRMD190 PKICPADPAF 200 FSFINNSDLW210 VANIETGEER220 RLTFCHQNVL233 DDPKSAGVAT243 FVIQEEFDRF 253 TGYWWCPTAS263 WEGLKTLRIL276 YEEVDESEVE286 VIHVPSPALE296 ERKTDSYRYP 306 RTGSKNPKIA316 LKLAEFQTDS326 QGKIVSTQEK336 ELVQPFSSLF346 PKVEYIARAG 356 WTRDGKYAWA366 MFLDRPQQWL376 QLVLLPPALF386 IPSTENEEQR396 LASARAVPRN 406 VQPYVVYEEV416 TNVWINVHDI426 FYPFPQLCFL442 RANECKTGFC452 HLYKVTAVLK 462 SQGYDWSEPF472 SPGEDEFKCP482 IKEEIALTSG492 EWEVLARHGS502 KIWVNEETKL 512 VYFQGTKDTP522 LEHHLYVVSY532 EAAGEIVRLT542 TPGFSHSCSM552 SQNFDMFVSH 562 YSSVSTPPCV572 HVYKLSGPDD582 DPLHKQPRFW592 ASMMEADYVP607 PEIFHFHTRS 617 DVRLYGMIYK627 PHALQPGKKH637 PTVLFVYGGP647 QVQLVNNSFK657 GIKYLRLNTL 667 ASLGYAVVVI677 DGRGSCQRGL687 RFEGALKNQM697 GQVEIEDQVE707 GLQFVAEKYG 717 FIDLSRVAIH727 GWSYGGFLSL737 MGLIHKPQVF747 KVAIAGAPVT757 VWMAYDTGYT 767 ERYMDVPENN777 QHGYEAGSVA787 LHVEKLPNEP797 NRLLILHGFL807 DENVHFFHTN 817 FLVSQLIRAG827 KPYQLQIYPN837 ERHSIRCPES847 GEHYEVTLLH857 FLQEYLHH |
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|
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ARG133
2.808
GLU248
2.320
GLU249
2.545
HIS500
4.160
TYR644
3.150
PRO647
4.147
GLN648
3.662
VAL649
4.146
LYS660
3.798
SER730
3.026
|
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| Ligand Name: Cysteine Sulfenic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295 | PDB:7ZXS | ||||
| Method | X-ray diffraction | Resolution | 1.81 Å | Mutation | No | [2] |
| PDB Sequence |
ARFQVQKHSW
31 DGLRSIIHGS41 RKYSGLIVNK51 APHDFQFVQK61 TDESGPHSHR71 LYYLGMPYGS 81 RENSLLYSEI91 PKKVRKEALL101 LLSWKQMLDH111 FQATPHHGVY121 SREEELLRER 131 KRLGVFGITS141 YDFHSESGLF151 LFQASNSLFH161 CRDGGKNGFM171 VSPMKPLEIK 181 TQCSGPRMDP191 KICPADPAFF201 SFINNSDLWV211 ANIETGEERR221 LTFCHQGLSN 231 VLDDPKSAGV241 ATFVIQEEFD251 RFTGYWWCPT261 ASWEGSEGLK271 TLRILYEEVD 281 ESEVEVIHVP291 SPALEERKTD301 SYRYPRTGSK311 NPKIALKLAE321 FQTDSQGKIV 331 STQEKELVQP341 FSSLFPKVEY351 IARAGWTRDG361 KYAWAMFLDR371 PQQWLQLVLL 381 PPALFIPSTE391 NEEQRLASAR401 AVPRNVQPYV411 VYEEVTNVWI421 NVHDIFYPFP 431 QSEGEDELCF441 LRANECKTGF451 CHLYKVTAVL461 KSQGYDWSEP471 FSPGEDEFKC 481 PIKEEIALTS491 GEWEVLARHG501 SKIWVNEETK511 LVYFQGTKDT521 PLEHHLYVVS 531 YEAAGEIVRL541 TTPGFSHSCS551 MSQNFDMFVS561 HYSSVSTPPC571 VHVYKLSGPD 581 DDPLHKQPRF591 WASMMEAASC601 PPDYVPPEIF611 HFHTRSDVRL621 YGMIYKPHAL 631 QPGKKHPTVL641 FVYGGPQVQL651 VNNSFKGIKY661 LRLNTLASLG671 YAVVVIDGRG 681 SCQRGLRFEG691 ALKNQMGQVE701 IEDQVEGLQF711 VAEKYGFIDL721 SRVAIHGWSY 731 GGFLSLMGLI741 HKPQVFKVAI751 AGAPVTVWMA761 YDTGYTERYM771 DVPENNQHGY 781 EAGSVALHVE791 KLPNEPNRLL801 ILHGFLDENV811 HFFHTNFLVS821 QLIRAGKPYQ 831 LQIYPNERHS841 IRPESGEHYE852 VTLLHFLQEY862 LHH
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| Ligand Name: (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile | Ligand Info | |||||
| Structure Description | DPP9 IN COMPLEX WITH LIGAND ICeD-1 | PDB:7SVN | ||||
| Method | X-ray diffraction | Resolution | 2.78 Å | Mutation | No | [3] |
| PDB Sequence |
DPAARFQVQK
28 HSWDGLRSII38 HGSRKAPHDF56 QFVQKTDESG66 PHSHRLYYLG76 MPYGSRENSL 86 LYSEIPKKVR96 LLLLSWKQML109 DHFQATPHHG119 VYSREEELLR129 ERKRLGVFGI 139 TSYDFHSESG149 LFLFQASNSL159 FHCRDGGKNG169 FMVSPMKPLE179 IKTQCSGPRM 189 DPKICPADPA199 FFSFINNSDL209 WVANIETGEE219 RRLTFCHQNV232 LDDPKSAGVA 242 TFVIQEEFDR252 FTGYWWCPTA262 SWEGSEGLKT272 LRILYEEVDE282 SEVEVIHVPS 292 PALEERKTDS302 YRYPRTGSKN312 PKIALKLAEF322 QTDSQGKIVS332 TQEKELVQPF 342 SSLFPKVEYI352 ARAGWTRDGK362 YAWAMFLDRP372 QQWLQLVLLP382 PALFIPSTEN 392 EEQRLASARA402 VPRNVQPYVV412 YEEVTNVWIN422 VHDIFYPFPQ432 SEDELCFLRA 444 NECKTGFCHL454 YKVTAVLKSQ464 GYDWSEPFSP474 GEDEFKCPIK484 EEIALTSGEW 494 EVLARHGSKI504 WVNEETKLVY514 FQGTKDTPLE524 HHLYVVSYEA534 AGEIVRLTTP 544 GFSHSCSMSQ554 NFDMFVSHYS564 SVSTPPCVHV574 YKLSGPDDDP584 LHKQPRFWAS 594 MMEADYVPPE609 IFHFHTRSDV619 RLYGMIYKPH629 ALQPGKKHPT639 VLFVYGGPQV 649 QLVNNSFKGI659 KYLRLNTLAS669 LGYAVVVIDG679 RGSCQRGLRF689 EGALKNQMGQ 699 VEIEDQVEGL709 QFVAEKYGFI719 DLSRVAIHGW729 SYGGFLSLMG739 LIHKPQVFKV 749 AIAGAPVTVW759 MAYDTGYTER769 YMDVPENNQH779 GYEAGSVALH789 VEKLPNEPNR 799 LLILHGFLDE809 NVHFFHTNFL819 VSQLIRAGKP829 YQLQIYPNER839 HSIRCPESGE 849 HYEVTLLHFL859 QEYLH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CW8 or .CW82 or .CW83 or :3CW8;style chemicals stick;color identity;select .A:133 or .A:248 or .A:249 or .A:500 or .A:644 or .A:647 or .A:648 or .A:649 or .A:730 or .A:731 or .A:756 or .A:759 or .A:762 or .A:766 or .A:810 or .A:811 or .A:840; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-ethyl-2-formyl-N-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide | Ligand Info | |||||
| Structure Description | Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295 | PDB:7ZXS | ||||
| Method | X-ray diffraction | Resolution | 1.81 Å | Mutation | No | [2] |
| PDB Sequence |
> Chain A
ARFQVQKHSW 31 DGLRSIIHGS41 RKYSGLIVNK51 APHDFQFVQK61 TDESGPHSHR71 LYYLGMPYGS 81 RENSLLYSEI91 PKKVRKEALL101 LLSWKQMLDH111 FQATPHHGVY121 SREEELLRER 131 KRLGVFGITS141 YDFHSESGLF151 LFQASNSLFH161 CRDGGKNGFM171 VSPMKPLEIK 181 TQCSGPRMDP191 KICPADPAFF201 SFINNSDLWV211 ANIETGEERR221 LTFCHQGLSN 231 VLDDPKSAGV241 ATFVIQEEFD251 RFTGYWWCPT261 ASWEGSEGLK271 TLRILYEEVD 281 ESEVEVIHVP291 SPALEERKTD301 SYRYPRTGSK311 NPKIALKLAE321 FQTDSQGKIV 331 STQEKELVQP341 FSSLFPKVEY351 IARAGWTRDG361 KYAWAMFLDR371 PQQWLQLVLL 381 PPALFIPSTE391 NEEQRLASAR401 AVPRNVQPYV411 VYEEVTNVWI421 NVHDIFYPFP 431 QSEGEDELCF441 LRANECKTGF451 CHLYKVTAVL461 KSQGYDWSEP471 FSPGEDEFKC 481 PIKEEIALTS491 GEWEVLARHG501 SKIWVNEETK511 LVYFQGTKDT521 PLEHHLYVVS 531 YEAAGEIVRL541 TTPGFSHSCS551 MSQNFDMFVS561 HYSSVSTPPC571 VHVYKLSGPD 581 DDPLHKQPRF591 WASMMEAASC601 PPDYVPPEIF611 HFHTRSDVRL621 YGMIYKPHAL 631 QPGKKHPTVL641 FVYGGPQVQL651 VNNSFKGIKY661 LRLNTLASLG671 YAVVVIDGRG 681 SCQRGLRFEG691 ALKNQMGQVE701 IEDQVEGLQF711 VAEKYGFIDL721 SRVAIHGWSY 731 GGFLSLMGLI741 HKPQVFKVAI751 AGAPVTVWMA761 YDTGYTERYM771 DVPENNQHGY 781 EAGSVALHVE791 KLPNEPNRLL801 ILHGFLDENV811 HFFHTNFLVS821 QLIRAGKPYQ 831 LQIYPNERHS841 IRPESGEHYE852 VTLLHFLQEY862 LHH> Chain B PAARFQVQKH 29 SWDGLRSIIH39 GSRKKAPHDF56 QFVQKTDESG66 PHSHRLYYLG76 MPYGSRENSL 86 LYSEIPKKVR96 KEALLLLSWK106 QMLDHFQATP116 HHGVYSREEE126 LLRERKRLGV 136 FGITSYDFHS146 ESGLFLFQAS156 NSLFHCRDGG166 KNGFMVSPMK176 PLEIKTQCSG 186 PRMDPKICPA196 DPAFFSFINN206 SDLWVANIET216 GEERRLTFCH226 QGLSNVLDDP 236 KSAGVATFVI246 QEEFDRFTGY256 WWCPTASWEG266 SEGLKTLRIL276 YEEVDESEVE 286 VIHVPSPALE296 ERKTDSYRYP306 RTGSKNPKIA316 LKLAEFQTDS326 QGKIVSTQEK 336 ELVQPFSSLF346 PKVEYIARAG356 WTRDGKYAWA366 MFLDRPQQWL376 QLVLLPPALF 386 IPSTENEEQR396 LASARAVPRN406 VQPYVVYEEV416 TNVWINVHDI426 FYPFPQSEGE 436 DELCFLRANE446 CKTGFCHLYK456 VTAVLKSQGY466 DWSEPFSPGE476 DEFKCPIKEE 486 IALTSGEWEV496 LARHGSKIWV506 NEETKLVYFQ516 GTKDTPLEHH526 LYVVSYEAAG 536 EIVRLTTPGF546 SHSCSMSQNF556 DMFVSHYSSV566 STPPCVHVYK576 LSGPDDDPLH 586 KQPRFWASMM596 EAASCPPDYV606 PPEIFHFHTR616 SDVRLYGMIY626 KPHALQPGKK 636 HPTVLFVYGG646 PQVQLVNNSF656 KGIKYLRLNT666 LASLGYAVVV676 IDGRGSCQRG 686 LRFEGALKNQ696 MGQVEIEDQV706 EGLQFVAEKY716 GFIDLSRVAI726 HGWSYGGFLS 736 LMGLIHKPQV746 FKVAIAGAPV756 TVWMAYDTGY766 TERYMDVPEN776 NQHGYEAGSV 786 ALHVEKLPNE796 PNRLLILHGF806 LDENVHFFHT816 NFLVSQLIRA826 GKPYQLQIYP 836 NERHSIRCPE846 SGEHYEVTLL856 HFLQEYLHH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KBO or .KBO2 or .KBO3 or :3KBO;style chemicals stick;color identity;select .A:133 or .A:248 or .A:249 or .A:500 or .A:644 or .A:648 or .A:649 or .A:660 or .A:729 or .A:730 or .A:731 or .A:756 or .A:759 or .A:762 or .A:766 or .A:810 or .A:811 or .A:840 or .B:133 or .B:248 or .B:249 or .B:500 or .B:644 or .B:647 or .B:648 or .B:649 or .B:660 or .B:729 or .B:730 or .B:731 or .B:756 or .B:759 or .B:762 or .B:766 or .B:810 or .B:811 or .B:840; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG133[A]
3.709
GLU248[A]
3.772
GLU249[A]
3.572
HIS500[A]
3.700
TYR644[A]
2.690
GLN648[A]
3.712
VAL649[A]
3.942
LYS660[A]
3.772
TRP729[A]
4.465
SER730[A]
1.454
TYR731[A]
2.909
VAL756[A]
3.748
TRP759[A]
4.643
TYR762[A]
3.319
TYR766[A]
3.915
ASN810[A]
3.383
VAL811[A]
3.751
HIS840[A]
3.433
ARG133[B]
3.881
GLU248[B]
3.707
GLU249[B]
3.687
HIS500[B]
3.482
TYR644[B]
2.676
PRO647[B]
4.935
GLN648[B]
3.569
VAL649[B]
3.801
LYS660[B]
4.407
TRP729[B]
4.359
SER730[B]
1.451
TYR731[B]
2.911
VAL756[B]
3.670
TRP759[B]
4.682
TYR762[B]
3.344
TYR766[B]
3.882
ASN810[B]
3.215
VAL811[B]
3.794
HIS840[B]
3.492
|
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| Ligand Name: [(2R)-1-[(2R)-2-amino-3-methylbutanoyl]pyrrolidin-2-yl]boronic acid | Ligand Info | |||||
| Structure Description | Cryo-EM structure of NLRP1-DPP9-VbP complex | PDB:6X6C | ||||
| Method | Electron microscopy | Resolution | 2.90 Å | Mutation | No | [4] |
| PDB Sequence |
DDPAARFQVQ
27 KHSWDGLRSI37 IHGSRKYSGL47 IVNKAPHDFQ57 FVQKTDESGP67 HSHRLYYLGM 77 PYGSRENSLL87 YSEIPKKVRK97 EALLLLSWKQ107 MLDHFQATPH117 HGVYSREEEL 127 LRERKRLGVF137 GITSYDFHSE147 SGLFLFQASN157 SLFHCRDGGK167 NGFMVSPMKP 177 LEIKTQCSGP187 RMDPKICPAD197 PAFFSFINNS207 DLWVANIETG217 EERRLTFCHQ 227 GLSNVLDDPK237 SAGVATFVIQ247 EEFDRFTGYW257 WCPTASWEGS267 EGLKTLRILY 277 EEVDESEVEV287 IHVPSPALEE297 RKTDSYRYPR307 TGSKNPKIAL317 KLAEFQTDSQ 327 GKIVSTQEKE337 LVQPFSSLFP347 KVEYIARAGW357 TRDGKYAWAM367 FLDRPQQWLQ 377 LVLLPPALFI387 PSTENEEQRL397 ASARAVPRNV407 QPYVVYEEVT417 NVWINVHDIF 427 YPFPQSEGED437 ELCFLRANEC447 KTGFCHLYKV457 TAVLKSQGYD467 WSEPFSPGED 477 EFKCPIKEEI487 ALTSGEWEVL497 ARHGSKIWVN507 EETKLVYFQG517 TKDTPLEHHL 527 YVVSYEAAGE537 IVRLTTPGFS547 HSCSMSQNFD557 MFVSHYSSVS567 TPPCVHVYKL 577 SGPDDDPLHK587 QPRFWASMME597 AASCPPDYVP607 PEIFHFHTRS617 DVRLYGMIYK 627 PHALQPGKKH637 PTVLFVYGGP647 QVQLVNNSFK657 GIKYLRLNTL667 ASLGYAVVVI 677 DGRGSCQRGL687 RFEGALKNQM697 GQVEIEDQVE707 GLQFVAEKYG717 FIDLSRVAIH 727 GWSYGGFLSL737 MGLIHKPQVF747 KVAIAGAPVT757 VWMAYDTGYT767 ERYMDVPENN 777 QHGYEAGSVA787 LHVEKLPNEP797 NRLLILHGFL807 DENVHFFHTN817 FLVSQLIRAG 827 KPYQLQIYPN837 ERHSIRCPES847 GEHYEVTLLH857 FLQEYL
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GK2 or .GK22 or .GK23 or :3GK2;style chemicals stick;color identity;select .A:133 or .A:248 or .A:249 or .A:644 or .A:648 or .A:730 or .A:731 or .A:756 or .A:759 or .A:762 or .A:763 or .A:766 or .A:810 or .A:811 or .A:840; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one | Ligand Info | |||||
| Structure Description | DPP9 IN COMPLEX WITH LIGAND ICeD-2 | PDB:7SVL | ||||
| Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [3] |
| PDB Sequence |
DPAARFQVQK
28 HSWDGLRSII38 HGSRKAPHDF56 QFVQKTDESG66 PHSHRLYYLG76 MPYGSRENSL 86 LYSEIPKKVR96 LLLLSWKQML109 DHFQATPHHG119 VYSREEELLR129 ERKRLGVFGI 139 TSYDFHSESG149 LFLFQASNSL159 FHCRDGGKNG169 FMVSPMKPLE179 IKTQCSGPRM 189 DPKICPADPA199 FFSFINNSDL209 WVANIETGEE219 RRLTFCHQVL233 DDPKSAGVAT 243 FVIQEEFDRF253 TGYWWCPTAS263 WEGSEGLKTL273 RILYEEVDES283 EVEVIHVPSP 293 ALEERKTDSY303 RYPRTGSKNP313 KIALKLAEFQ323 TDSQGKIVST333 QEKELVQPFS 343 SLFPKVEYIA353 RAGWTRDGKY363 AWAMFLDRPQ373 QWLQLVLLPP383 ALFIPSTENE 393 EQRLASARAV403 PRNVQPYVVY413 EEVTNVWINV423 HDIFYPFPQS433 EDELCFLRAN 445 ECKTGFCHLY455 KVTAVLKSQG465 YDWSEPFSPG475 EDEFKCPIKE485 EIALTSGEWE 495 VLARHGSKIW505 VNEETKLVYF515 QGTKDTPLEH525 HLYVVSYEAA535 GEIVRLTTPG 545 FSHSCSMSQN555 FDMFVSHYSS565 VSTPPCVHVY575 KLSGPDDDPL585 HKQPRFWASM 595 MEADYVPPEI610 FHFHTRSDVR620 LYGMIYKPHA630 LQPGKKHPTV640 LFVYGGPQVQ 650 LVNNSFKGIK660 YLRLNTLASL670 GYAVVVIDGR680 GSCQRGLRFE690 GALKNQMGQV 700 EIEDQVEGLQ710 FVAEKYGFID720 LSRVAIHGWS730 YGGFLSLMGL740 IHKPQVFKVA 750 IAGAPVTVWM760 AYDTGYTERY770 MDVPENNQHG780 YEAGSVALHV790 EKLPNEPNRL 800 LILHGFLDEN810 VHFFHTNFLV820 SQLIRAGKPY830 QLQIYPNERH840 SIRCPESGEH 850 YEVTLLHFLQ860 EYLH
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .D06 or .D062 or .D063 or :3D06;style chemicals stick;color identity;select .A:133 or .A:248 or .A:249 or .A:500 or .A:644 or .A:647 or .A:648 or .A:649 or .A:730 or .A:731 or .A:734 or .A:754 or .A:755 or .A:756 or .A:759 or .A:762 or .A:766 or .A:810 or .A:811 or .A:840; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG133
2.743
GLU248
2.707
GLU249
2.802
HIS500
3.353
TYR644
3.503
PRO647
4.809
GLN648
3.449
VAL649
3.416
SER730
3.156
TYR731
3.232
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer. Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1437-E1445. | ||||
| REF 2 | Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9. Angew Chem Int Ed Engl. 2022 Nov 21;61(47):e202210498. | ||||
| REF 3 | A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells. ACS Chem Biol. 2022 Sep 16;17(9):2595-2604. | ||||
| REF 4 | DPP9 sequesters the C?terminus of NLRP1 to repress inflammasome activation. Nature. 2021 Apr;592(7856):778-783. | ||||
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