Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T10383 | Target Info | |||
| Target Name | Phospholipase D2 (PLD2) | ||||
| Synonyms | hPLD2; Phosphatidylcholine-hydrolyzing phospholipase D2; PLD1C; PLD 2; Choline phosphatase 2 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PLD2 | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Halopemide | Ligand Info | |||||
| Structure Description | Structure of compound 1 (halopemide) bound human Phospholipase D2 catalytic domain | PDB:6OHP | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [1] |
| PDB Sequence |
FLQLHRHDSY
326 APPRPGTLAR336 WFVNGAGYFA346 AVADAILRAQ356 EEIFITDWWL366 SPEVYLKRPA 376 HSDDWRLDIM386 LKRKAEEGVR396 VSILLFKEVE406 LALGINSGYS416 KRALMLLHPN 426 IKVMRHPDQV436 TLWAHHEKLL446 VVDQVVAFLG456 GLDLAYGRWD466 DLHYRLTDLG 476 DLSHNQFFWL507 GKDYSNLITK517 DWVQLDRPFE527 DFIDRETTPR537 MPWRDVGVVV 547 HGLPARDLAR557 HFIQRWNFTK567 TTKAKKTPTY578 PYLLPKSTST588 FTLPGGQCTT 603 VQVLRSVDRW613 SAGTLENSIL623 NAYLHTIRES633 QHFLYIENQF643 FISCSDGRTV 653 LNKVGDEIVD663 RILKAHKQGW673 CYRVYVLLPL683 LPGFEGDIST693 GGGNSIQAIL 703 HFTYRTLCRG713 EYSILHRLKA723 AMGTAWRDYI733 SICGLRTHGE743 LGGHPVSELI 753 YIHSKVLIAD763 DRTVIIGSAN773 INDRSLLGKR783 DSELAVLIED793 TETEPSLMNG 803 AEYQAGRFAL813 SLRKHCFGVI823 LGANTRPDLD833 LRDPICDDFF843 QLWQDMAESN 853 ANIYEQIFRC863 LPSNATRSLR873 TLREYVAVEP883 LATVSPPLAR893 SELTQVQGHL 903 VHFPLKFLED913 ESLLPPGMIP928 LEVWT
|
|||||
|
|
TRP364
3.458
TRP365
3.326
PHE402
4.652
LEU409
3.623
GLY410
3.187
ILE411
3.653
LEU438
3.921
TRP439
4.937
ALA440
3.624
HIS442
3.218
ARG464
2.484
LEU514
3.430
ASP518
3.667
|
|||||
| Ligand Name: Phosphonotyrosine | Ligand Info | |||||
| Structure Description | Structure of compound 1 (halopemide) bound human Phospholipase D2 catalytic domain | PDB:6OHP | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [1] |
| PDB Sequence |
FLQLHRHDSY
326 APPRPGTLAR336 WFVNGAGYFA346 AVADAILRAQ356 EEIFITDWWL366 SPEVYLKRPA 376 HSDDWRLDIM386 LKRKAEEGVR396 VSILLFKEVE406 LALGINSGYS416 KRALMLLHPN 426 IKVMRHPDQV436 TLWAHHEKLL446 VVDQVVAFLG456 GLDLAYGRWD466 DLHYRLTDLG 476 DLSHNQFFWL507 GKDYSNLITK517 DWVQLDRPFE527 DFIDRETTPR537 MPWRDVGVVV 547 HGLPARDLAR557 HFIQRWNFTK567 TTKAKKTPTY578 PYLLPKSTST588 FTLPGGQCTT 603 VQVLRSVDRW613 SAGTLENSIL623 NAYLHTIRES633 QHFLYIENQF643 FISCSDGRTV 653 LNKVGDEIVD663 RILKAHKQGW673 CYRVYVLLPL683 LPGFEGDIST693 GGGNSIQAIL 703 HFTYRTLCRG713 EYSILHRLKA723 AMGTAWRDYI733 SICGLRTHGE743 LGGHPVSELI 753 YIHSKVLIAD763 DRTVIIGSAN773 INDRSLLGKR783 DSELAVLIED793 TETEPSLMNG 803 AEYQAGRFAL813 SLRKHCFGVI823 LGANTRPDLD833 LRDPICDDFF843 QLWQDMAESN 853 ANIYEQIFRC863 LPSNATRSLR873 TLREYVAVEP883 LATVSPPLAR893 SELTQVQGHL 903 VHFPLKFLED913 ESLLPPGMIP928 LEVWT
|
|||||
|
|
||||||
| Ligand Name: Tungstate | Ligand Info | |||||
| Structure Description | Structure of tungstate bound human Phospholipase D2 catalytic domain | PDB:6OHM | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
DFLQLHRHDS
325 YAPPRPGTLA335 RWFVNGAGYF345 AAVADAILRA355 QEEIFITDWW365 LSPEVYLKRP 375 AHSDDWRLDI385 MLKRKAEEGV395 RVSILLFKEV405 ELGINSGYSK417 RALMLLHPNI 427 KVMRHPDQVT437 LWAHHEKLLV447 VDQVVAFLGG457 LDLAYGRWDD467 LHYRLTDLGP 497 DLSHNQFFWL507 GKDYSNLITK517 DWVQLDRPFE527 DFIDRETTPR537 MPWRDVGVVV 547 HGLPARDLAR557 HFIQRWNFTK567 TTKAKYKTPT577 YPYLLPKSPG598 GQCTTVQVLR 608 SVDRWSAGTL618 ENSILNAYLH628 TIRESQHFLY638 IENQFFISCS648 DGRTVLNKVG 658 DEIVDRILKA668 HKQGWCYRVY678 VLLPLLPGFE688 GDISTGGGNS698 IQAILHFTYR 708 TLCRGEYSIL718 HRLKAAMGTA728 WRDYISICGL738 RTHGELGGHP748 VSELIYIHSK 758 VLIADDRTVI768 IGSANINDRS778 LLGKRDSELA788 VLIEDTETEP798 SLMNGAEYQA 808 GRFALSLRKH818 CFGVILGPDL832 DLRDPICDDF842 FQLWQDMAES852 NANIYEQIFR 862 CLPSNATRSL872 RTLREYVAVE882 PLATVSPPLA892 RSELTQVQGH902 LVHFPLKFLE 912 DESLLGMIPL929 EVWT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WO4 or .WO42 or .WO43 or :3WO4;style chemicals stick;color identity;select .A:364 or .A:442 or .A:444 or .A:459 or .A:464 or .A:642 or .A:756 or .A:758 or .A:771 or .A:773; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-fluoro-N-{(2S)-1-[4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)piperidin-1-yl]propan-2-yl}benzamide | Ligand Info | |||||
| Structure Description | Structure of compound 4 bound human Phospholipase D2 catalytic domain | PDB:6OHQ | ||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [1] |
| PDB Sequence |
RDFLQLHRHD
324 SYAPPRPGTL334 ARWFVNGAGY344 FAAVADAILR354 AQEEIFITDW364 WLSPEVYLKR 374 PAHSDDWRLD384 IMLKRKAEEG394 VRVSILLFKE404 VELGINSGYS416 KRALMLLHPN 426 IKVMRHPDQV436 TLWAHHEKLL446 VVDQVVAFLG456 GLDLAYGRWD466 DLHYRLTDLG 476 DLSHNQFFWL507 GKDYSNLITK517 DWVQLDRPFE527 DFIDRETTPR537 MPWRDVGVVV 547 HGLPARDLAR557 HFIQRWNFTK567 TTKAKYKTPT577 YPYLLPKSTS587 TANGGQCTTV 604 QVLRSVDRWS614 AGTLENSILN624 AYLHTIRESQ634 HFLYIENQFF644 ISCSDGRTVL 654 NKVGDEIVDR664 ILKAHKQGWC674 YRVYVLLPLL684 PGFEGDISTG694 GGNSIQAILH 704 FTYRTLCRGE714 YSILHRLKAA724 MGTAWRDYIS734 ICGLRTHGEL744 GGHPVSELIY 754 IHSKVLIADD764 RTVIIGSANI774 NDRSLLGKRD784 SELAVLIEDT794 ETEPSLMNGA 804 EYQAGRFALS814 LRKHCFGVIL824 GPDLDLRDPI838 CDDFFQLWQD848 MAESNANIYE 858 QIFRCLPSNA868 TRSLRTLREY878 VAVEPLATVS888 PPLARSELTQ898 VQGHLVHFPL 908 KFLEDESLLP918 PGMIPLEVWT933
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MKA or .MKA2 or .MKA3 or :3MKA;style chemicals stick;color identity;select .A:364 or .A:365 or .A:409 or .A:410 or .A:411 or .A:440 or .A:442 or .A:464 or .A:514 or .A:518 or .A:519 or .A:540 or .A:642 or .A:643 or .A:686 or .A:687 or .A:754 or .A:756 or .A:758 or .A:773 or .A:777 or .A:784; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
TRP364
3.322
TRP365
3.346
LEU409
4.479
GLY410
3.305
ILE411
3.577
ALA440
4.223
HIS442
3.157
ARG464
2.512
LEU514
1.493
ASP518
3.531
TRP519
3.502
|
|||||
| Ligand Name: (S)-4-bromo-N-(1-(1-(3-fluorophenyl)-4-oxo-1,3,8-triazaspiro[4.5]decan-8-yl)propan-2-yl)benzamide | Ligand Info | |||||
| Structure Description | Structure of compound 3 (ML299) bound human Phospholipase D2 catalytic domain | PDB:6OHS | ||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | No | [1] |
| PDB Sequence |
RDFLQLHRHD
324 SYAPPRPGTL334 ARWFVNGAGY344 FAAVADAILR354 AQEEIFITDW364 WLSPEVYLKR 374 PAHSDDWRLD384 IMLKRKAEEG394 VRVSILLFKE404 VELGINSGYS416 KRALMLLHPN 426 IKVMRHPDQV436 TLWAHHEKLL446 VVDQVVAFLG456 GLDLAYGRWD466 DLHYRLTDLG 476 DLSHNQFFWL507 GKDYSNLITK517 DWVQLDRPFE527 DFIDRETTPR537 MPWRDVGVVV 547 HGLPARDLAR557 HFIQRWNFTK567 TTKAKYKTPT577 YPYLLPKSTS587 TLPGGQCTTV 604 QVLRSVDRWS614 AGTLENSILN624 AYLHTIRESQ634 HFLYIENQFF644 ISCSDGRTVL 654 NKVGDEIVDR664 ILKAHKQGWC674 YRVYVLLPLL684 PGFEGDISTG694 GGNSIQAILH 704 FTYRTLCRGE714 YSILHRLKAA724 MGTAWRDYIS734 ICGLRTHGEL744 GGHPVSELIY 754 IHSKVLIADD764 RTVIIGSANI774 NDRSLLGKRD784 SELAVLIEDT794 ETEPSLMNGA 804 EYQAGRFALS814 LRKHCFGVIL824 GANTRPDLDL834 RDPICDDFFQ844 LWQDMAESNA 854 NIYEQIFRCL864 PSNATRSLRT874 LREYVAVEPL884 ATVSPPLARS894 ELTQVQGHLV 904 HFPLKFLEDE914 SLLPPGMIPL929 EVWT
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MJY or .MJY2 or .MJY3 or :3MJY;style chemicals stick;color identity;select .A:364 or .A:365 or .A:402 or .A:409 or .A:410 or .A:411 or .A:438 or .A:439 or .A:440 or .A:442 or .A:464 or .A:514 or .A:518 or .A:519 or .A:540 or .A:642 or .A:643 or .A:686 or .A:687 or .A:754 or .A:756 or .A:773 or .A:777 or .A:778 or .A:784 or .A:786; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
TRP364
3.395
TRP365
3.440
PHE402
3.835
LEU409
3.446
GLY410
3.446
ILE411
3.586
LEU438
4.109
TRP439
4.911
ALA440
3.749
HIS442
3.137
ARG464
2.925
LEU514
3.178
ASP518
3.009
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Human PLD structures enable drug design and characterization of isoenzyme selectivity. Nat Chem Biol. 2020 Apr;16(4):391-399. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.