Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T08123 | Target Info | |||
| Target Name | Leucine-rich repeat kinase 2 (LRRK2) | ||||
| Synonyms | PARK8; Leucine-rich repeat serine/threonine-protein kinase 2; Dardarin | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | LRRK2 | ||||
| Biochemical Class | Kinase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Guanosine-5'-Diphosphate | Ligand Info | |||
| Canonical SMILES | C1=NC2=C(N1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N | ||||
| InChI | 1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 | ||||
| InChIKey | QGWNDRXFNXRZMB-UUOKFMHZSA-N | ||||
| PubChem Compound ID | 135398619 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7LI4 Structure of LRRK2 after symmetry expansion | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | Yes | [1] |
| PDB Sequence |
GIQKCGLKVI
567 SSIVHFPDAL577 GAMDSVLHTL593 QMYPDDQEIQ603 CLGLSLIGYG624 HLLAKILVSS 634 LYRFKDVAEI644 QTKGFQTILA654 ILKLSASFSK664 LLVHHSFDLV674 IFHQMSSNIM 684 EQKDQQFLNL694 CCKCFAKVAM704 DDYLKNVMLE714 RACDQNNSIM724 VECLLLLGAD 734 ANQAKEGSSL744 ICQVCEKESS754 PKLVELLLNS764 GSREQDVRKA774 LTISIGKGDS 784 QIISLLLRRL794 ALDVANNSIC804 LGGFCIGKVE814 PSWLGPLFPD824 KTSNLRKQTN 834 IASTLARMVI844 RYQMKSAVEE854 REYITSLDLS990 ANELRDIDAL1000 SQKCCISVHL 1010 EHLEKLELHQ1020 NALTSFPQQL1030 CETLKSLTHL1040 DLHSNKFTSF1050 PSYLLKMSCI 1060 ANLDVSRNDI1070 GPSVVLDPTV1080 KCPTLKQFNL1090 SYNQLSFVPE1100 NLTDVVEKLE 1110 QLILEGNKIS1120 GICSPLRLKE1130 LKILNLSKNH1140 ISSLSENFLE1150 ACPKVESFSA 1160 RMNFLAAMPF1170 LPPSMTILKL1180 SQNKFSCIPE1190 AILNLPHLRS1200 LDMSSNDIQY 1210 LPGPAHWKSL1220 NLRELLFSHN1230 QISILDLSEK1240 AYLWSRVEKL1250 HLSHNKLKEI 1260 PPEIGCLENL1270 TSLDVSYNLE1280 LRSFPNEMGK1290 LSKIWDLPLD1300 ELHLNFDFKH 1310 IGCKAKDIIR1320 FLQQRLKKAV1330 PYNRMKLMIV1340 GNTGSGKTTL1350 LQQLMKTKKS 1360 DLGMQSATVG1370 IDVKDWPIQI1380 RDKRKRDLVL1390 NVWDFAGREE1400 FYSTHPHFMT 1410 QRALYLAVYD1420 LSKGQAEVDA1430 MKPWLFNIKA1440 RASSSPVILV1450 GTHLDVSKAC 1465 MSKITKELLN1475 KRGFPAIRDY1485 HFVNATEESD1495 ALAKLRKTII1505 NESLNFKIRD 1515 QLVVGQLIPD1525 CYVELEKIIL1535 SERKNVPIEF1545 PVIDRKRLLQ1555 LVRENQLQLD 1565 ENELPHAVHF1575 LNESGVLLHF1585 QDPALQLSDL1595 YFVEPKWLCK1605 IMAQILTVKV 1615 EGCPKHPKGI1625 ISRRDPKNYM1646 TQYFKLLEKF1656 QIALVPSSLS1674 DHRPVIELPH 1684 CENSEIIIRL1694 YEMPYFPMGF1704 WSRLINRLLE1714 ISPYMLALRP1729 NRMYWRQGIY 1739 LNWSPEAYCL1749 VGSEVLDNHP1759 ESFLKITVPS1769 CRKGCILLGQ1779 VVDHIDSLME 1789 EWFPGLLEID1799 ICGEGETLLK1809 KWALYSFNDG1819 EEHQKILLDD1829 LMKKAEEGDL 1839 LVNPDQPRLT1849 IPISQIAPDL1859 ILADLPRNIM1869 LNNDELEFEQ1879 APEFLLGDGS 1889 FGSVYRAAYE1899 GEEVAVKIFN1909 KHTSLRLLRQ1919 ELVVLCHLHH1929 PSLISLLAAG 1939 IRPRMLVMEL1949 ASKGSLDRLL1959 QQDKASLTRT1969 LQHRIALHVA1979 DGLRYLHSAM 1989 IIYRDLKPHN1999 VLLFTLYPNA2009 AIIAKIADYG2019 IAQYCCRMTS2032 EGTPGFRAPE 2042 VARGNVIYNQ2052 QADVYSFGLL2062 LYDILTTGGR2072 IVEGLKFPNE2082 FDELEIQGKL 2092 PDPVKEYGCA2102 PWPMVEKLIK2112 QCLKENPQER2122 PTSAQVFDIL2132 NSAELVCLTR 2142 RILLPKNVIV2152 ECMVATHHNS2162 RNASIWLGCG2172 HTDRGQLSFL2182 DLNTEGYTSE 2192 EVADSRILCL2202 ALVHLPVEKE2212 SWIVSGTQSG2222 TLLVINTEDG2232 KKRHTLEKMT 2242 DSVTCLYCNS2252 FSKQSKQKNF2262 LLVGTADGKL2272 AIFEDKTVKL2282 KGAAPLKILN 2292 IGNVSTPLMC2302 LSESTNSTER2312 NVMWGGCGTK2322 IFSFSNDFTI2332 QKLIETRTSQ 2342 LFSYAAFSDS2352 NIITVVVDTA2362 LYIAKQNSPV2372 VEVWDKKTEK2382 LCGLIDCVHF 2392 LREVTVKENK2402 ESKHKMSYSG2412 RVKTLCLQKN2422 TALWIGTGGG2432 HILLLDLSTR 2442 RLIRVIYNFC2452 NSVRVMMTAQ2462 LGSLKNVMLV2472 LGYNRKNTEG2482 TQKQKEIQSC 2492 LTVWDINLPH2502 EVQNLEKHIE2512 VRKELAEKMR2522 RTSVE
|
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|
|
ASN1342
4.741
THR1343
3.751
GLY1344
3.313
SER1345
3.127
GLY1346
3.598
LYS1347
3.442
THR1348
2.835
THR1349
3.356
GLN1365
3.548
SER1366
4.718
ALA1367
3.846
|
|||||
| PDB ID: 7LHT Structure of the LRRK2 dimer | ||||||
| Method | Electron microscopy | Resolution | 3.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
GIQKCGLKVI
567 SSIVHFPDAL577 GAMDSVLHTL593 QMYPDDQEIQ603 CLGLSLIGYG624 HLLAKILVSS 634 LYRFKDVAEI644 QTKGFQTILA654 ILKLSASFSK664 LLVHHSFDLV674 IFHQMSSNIM 684 EQKDQQFLNL694 CCKCFAKVAM704 DDYLKNVMLE714 RACDQNNSIM724 VECLLLLGAD 734 ANQAKEGSSL744 ICQVCEKESS754 PKLVELLLNS764 GSREQDVRKA774 LTISIGKGDS 784 QIISLLLRRL794 ALDVANNSIC804 LGGFCIGKVE814 PSWLGPLFPD824 KTSNLRKQTN 834 IASTLARMVI844 RYQMKSAVEE854 REYITSLDLS990 ANELRDIDAL1000 SQKCCISVHL 1010 EHLEKLELHQ1020 NALTSFPQQL1030 CETLKSLTHL1040 DLHSNKFTSF1050 PSYLLKMSCI 1060 ANLDVSRNDI1070 GPSVVLDPTV1080 KCPTLKQFNL1090 SYNQLSFVPE1100 NLTDVVEKLE 1110 QLILEGNKIS1120 GICSPLRLKE1130 LKILNLSKNH1140 ISSLSENFLE1150 ACPKVESFSA 1160 RMNFLAAMPF1170 LPPSMTILKL1180 SQNKFSCIPE1190 AILNLPHLRS1200 LDMSSNDIQY 1210 LPGPAHWKSL1220 NLRELLFSHN1230 QISILDLSEK1240 AYLWSRVEKL1250 HLSHNKLKEI 1260 PPEIGCLENL1270 TSLDVSYNLE1280 LRSFPNEMGK1290 LSKIWDLPLD1300 ELHLNFDFKH 1310 IGCKAKDIIR1320 FLQQRLKKAV1330 PYNRMKLMIV1340 GNTGSGKTTL1350 LQQLMKTKKS 1360 DLGMQSATVG1370 IDVKDWPIQI1380 RDKRKRDLVL1390 NVWDFAGREE1400 FYSTHPHFMT 1410 QRALYLAVYD1420 LSKGQAEVDA1430 MKPWLFNIKA1440 RASSSPVILV1450 GTHLDVSKAC 1465 MSKITKELLN1475 KRGFPAIRDY1485 HFVNATEESD1495 ALAKLRKTII1505 NESLNFKIRD 1515 QLVVGQLIPD1525 CYVELEKIIL1535 SERKNVPIEF1545 PVIDRKRLLQ1555 LVRENQLQLD 1565 ENELPHAVHF1575 LNESGVLLHF1585 QDPALQLSDL1595 YFVEPKWLCK1605 IMAQILTVKV 1615 EGCPKHPKGI1625 ISRRDPKNYM1646 TQYFKLLEKF1656 QIALVPSSLS1674 DHRPVIELPH 1684 CENSEIIIRL1694 YEMPYFPMGF1704 WSRLINRLLE1714 ISPYMLALRP1729 NRMYWRQGIY 1739 LNWSPEAYCL1749 VGSEVLDNHP1759 ESFLKITVPS1769 CRKGCILLGQ1779 VVDHIDSLME 1789 EWFPGLLEID1799 ICGEGETLLK1809 KWALYSFNDG1819 EEHQKILLDD1829 LMKKAEEGDL 1839 LVNPDQPRLT1849 IPISQIAPDL1859 ILADLPRNIM1869 LNNDELEFEQ1879 APEFLLGDGS 1889 FGSVYRAAYE1899 GEEVAVKIFN1909 KHTSLRLLRQ1919 ELVVLCHLHH1929 PSLISLLAAG 1939 IRPRMLVMEL1949 ASKGSLDRLL1959 QQDKASLTRT1969 LQHRIALHVA1979 DGLRYLHSAM 1989 IIYRDLKPHN1999 VLLFTLYPNA2009 AIIAKIADYG2019 IAQYCCRMTS2032 EGTPGFRAPE 2042 VARGNVIYNQ2052 QADVYSFGLL2062 LYDILTTGGR2072 IVEGLKFPNE2082 FDELEIQGKL 2092 PDPVKEYGCA2102 PWPMVEKLIK2112 QCLKENPQER2122 PTSAQVFDIL2132 NSAELVCLTR 2142 RILLPKNVIV2152 ECMVATHHNS2162 RNASIWLGCG2172 HTDRGQLSFL2182 DLNTEGYTSE 2192 EVADSRILCL2202 ALVHLPVEKE2212 SWIVSGTQSG2222 TLLVINTEDG2232 KKRHTLEKMT 2242 DSVTCLYCNS2252 FSKQSKQKNF2262 LLVGTADGKL2272 AIFEDKTVKL2282 KGAAPLKILN 2292 IGNVSTPLMC2302 LSESTNSTER2312 NVMWGGCGTK2322 IFSFSNDFTI2332 QKLIETRTSQ 2342 LFSYAAFSDS2352 NIITVVVDTA2362 LYIAKQNSPV2372 VEVWDKKTEK2382 LCGLIDCVHF 2392 LREVTVKENK2402 ESKHKMSYSG2412 RVKTLCLQKN2422 TALWIGTGGG2432 HILLLDLSTR 2442 RLIRVIYNFC2452 NSVRVMMTAQ2462 LGSLKNVMLV2472 LGYNRKNTEG2482 TQKQKEIQSC 2492 LTVWDINLPH2502 EVQNLEKHIE2512 VRKELAEKMR2522 RTSVE
|
|||||
|
|
THR1343
4.593
GLY1344
3.716
SER1345
2.721
GLY1346
3.885
LYS1347
3.162
THR1348
2.862
THR1349
3.038
GLN1365
3.787
SER1366
4.967
ALA1367
4.135
THR1368
2.569
|
|||||
| PDB ID: 7LHW Structure of the LRRK2 monomer | ||||||
| Method | Electron microscopy | Resolution | 3.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
NDIHKLVLAA
549 LNRFIGNPGI559 QKCGLKVISS569 IVHFPDALGA585 MDSVLHTLQM595 YPDDQEIQCL 605 GLSLIGYGHL626 LAKILVSSLY636 RFKDVAEIQT646 KGFQTILAIL656 KLSASFSKLL 666 VHHSFDLVIF676 HQMSSNIMEQ686 KDQQFLNLCC696 KCFAKVAMDD706 YLKNVMLERA 716 CDQNNSIMVE726 CLLLLGADAN736 QAKEGSSLIC746 QVCEKESSPK756 LVELLLNSGS 766 REQDVRKALT776 ISIGKGDSQI786 ISLLLRRLAL796 DVANNSICLG806 GFCIGKVEPS 816 WLGPLFPDKT826 SNLRKQTNIA836 STLARMVIRY846 QMKSAVEERE982 YITSLDLSAN 992 ELRDIDALSQ1002 KCCISVHLEH1012 LEKLELHQNA1022 LTSFPQQLCE1032 TLKSLTHLDL 1042 HSNKFTSFPS1052 YLLKMSCIAN1062 LDVSRNDIGP1072 SVVLDPTVKC1082 PTLKQFNLSY 1092 NQLSFVPENL1102 TDVVEKLEQL1112 ILEGNKISGI1122 CSPLRLKELK1132 ILNLSKNHIS 1142 SLSENFLEAC1152 PKVESFSARM1162 NFLAAMPFLP1172 PSMTILKLSQ1182 NKFSCIPEAI 1192 LNLPHLRSLD1202 MSSNDIQYLP1212 GPAHWKSLNL1222 RELLFSHNQI1232 SILDLSEKAY 1242 LWSRVEKLHL1252 SHNKLKEIPP1262 EIGCLENLTS1272 LDVSYNLELR1282 SFPNEMGKLS 1292 KIWDLPLDEL1302 HLNFDFKHIG1312 CKAKDIIRFL1322 QQRLKKAVPY1332 NRMKLMIVGN 1342 TGSGKTTLLQ1352 QLMKTKKSDL1362 GMQSATVGID1372 VKDWPIQIRD1382 KRKRDLVLNV 1392 WDFAGREEFY1402 STHPHFMTQR1412 ALYLAVYDLS1422 KGQAEVDAMK1432 PWLFNIKARA 1442 SSSPVILVGT1452 HLDVSKACMS1467 KITKELLNKR1477 GFPAIRDYHF1487 VNATEESDAL 1497 AKLRKTIINE1507 SLNFKIRDQL1517 VVGQLIPDCY1527 VELEKIILSE1537 RKNVPIEFPV 1547 IDRKRLLQLV1557 RENQLQLDEN1567 ELPHAVHFLN1577 ESGVLLHFQD1587 PALQLSDLYF 1597 VEPKWLCKIM1607 AQILTVKVEG1617 CPKHPKGIIS1627 RRDPKNYMTQ1648 YFKLLEKFQI 1658 ALVPSSLSDH1676 RPVIELPHCE1686 NSEIIIRLYE1696 MPYFPMGFWS1706 RLINRLLEIS 1716 PYMLALRPNR1731 MYWRQGIYLN1741 WSPEAYCLVG1751 SEVLDNHPES1761 FLKITVPSCR 1771 KGCILLGQVV1781 DHIDSLMEEW1791 FPGLLEIDIC1801 GEGETLLKKW1811 ALYSFNDGEE 1821 HQKILLDDLM1831 KKAEEGDLLV1841 NPDQPRLTIP1851 ISQIAPDLIL1861 ADLPRNIMLN 1871 NDELEFEQAP1881 EFLLGDGSFG1891 SVYRAAYEGE1901 EVAVKIFNKH1911 TSLRLLRQEL 1921 VVLCHLHHPS1931 LISLLAAGIR1941 PRMLVMELAS1951 KGSLDRLLQQ1961 DKASLTRTLQ 1971 HRIALHVADG1981 LRYLHSAMII1991 YRDLKPHNVL2001 LFTLYPNAAI2011 IAKIADYGIA 2021 QYCCRMTSEG2034 TPGFRAPEVA2044 RGNVIYNQQA2054 DVYSFGLLLY2064 DILTTGGRIV 2074 EGLKFPNEFD2084 ELEIQGKLPD2094 PVKEYGCAPW2104 PMVEKLIKQC2114 LKENPQERPT 2124 SAQVFDILNS2134 AELVCLTRRI2144 LLPKNVIVEC2154 MVATHHNSRN2164 ASIWLGCGHT 2174 DRGQLSFLDL2184 NTEGYTSEEV2194 ADSRILCLAL2204 VHLPVEKESW2214 IVSGTQSGTL 2224 LVINTEDGKK2234 RHTLEKMTDS2244 VTCLYCNSFS2254 KQSKQKNFLL2264 VGTADGKLAI 2274 FEDKTVKLKG2284 AAPLKILNIG2294 NVSTPLMCLS2304 ESTNSTERNV2314 MWGGCGTKIF 2324 SFSNDFTIQK2334 LIETRTSQLF2344 SYAAFSDSNI2354 ITVVVDTALY2364 IAKQNSPVVE 2374 VWDKKTEKLC2384 GLIDCVHFLR2394 EVTVKENKES2404 KHKMSYSGRV2414 KTLCLQKNTA 2424 LWIGTGGGHI2434 LLLDLSTRRL2444 IRVIYNFCNS2454 VRVMMTAQLG2464 SLKNVMLVLG 2474 YNRKNTEGTQ2484 KQKEIQSCLT2494 VWDINLPHEV2504 QNLEKHIEVR2514 KELAEKMRRT 2524 SVE
|
|||||
|
|
THR1343
3.809
GLY1344
3.638
SER1345
2.800
GLY1346
3.757
LYS1347
3.164
THR1348
2.302
THR1349
3.406
GLN1365
4.105
SER1366
4.858
ALA1367
3.806
THR1368
2.725
|
|||||
| PDB ID: 7LI3 Structure of the LRRK2 G2019S mutant | ||||||
| Method | Electron microscopy | Resolution | 3.80 Å | Mutation | Yes | [1] |
| PDB Sequence |
GIQKCGLKVI
567 SSIVHFPDAL577 GAMDSVLHTL593 QMYPDDQEIQ603 CLGLSLIGYG624 HLLAKILVSS 634 LYRFKDVAEI644 QTKGFQTILA654 ILKLSASFSK664 LLVHHSFDLV674 IFHQMSSNIM 684 EQKDQQFLNL694 CCKCFAKVAM704 DDYLKNVMLE714 RACDQNNSIM724 VECLLLLGAD 734 ANQAKEGSSL744 ICQVCEKESS754 PKLVELLLNS764 GSREQDVRKA774 LTISIGKGDS 784 QIISLLLRRL794 ALDVANNSIC804 LGGFCIGKVE814 PSWLGPLFPD824 KTSNLRKQTN 834 IASTLARMVI844 RYQMKSAVEE854 REYITSLDLS990 ANELRDIDAL1000 SQKCCISVHL 1010 EHLEKLELHQ1020 NALTSFPQQL1030 CETLKSLTHL1040 DLHSNKFTSF1050 PSYLLKMSCI 1060 ANLDVSRNDI1070 GPSVVLDPTV1080 KCPTLKQFNL1090 SYNQLSFVPE1100 NLTDVVEKLE 1110 QLILEGNKIS1120 GICSPLRLKE1130 LKILNLSKNH1140 ISSLSENFLE1150 ACPKVESFSA 1160 RMNFLAAMPF1170 LPPSMTILKL1180 SQNKFSCIPE1190 AILNLPHLRS1200 LDMSSNDIQY 1210 LPGPAHWKSL1220 NLRELLFSHN1230 QISILDLSEK1240 AYLWSRVEKL1250 HLSHNKLKEI 1260 PPEIGCLENL1270 TSLDVSYNLE1280 LRSFPNEMGK1290 LSKIWDLPLD1300 ELHLNFDFKH 1310 IGCKAKDIIR1320 FLQQRLKKAV1330 PYNRMKLMIV1340 GNTGSGKTTL1350 LQQLMKTKKS 1360 DLGMQSATVG1370 IDVKDWPIQI1380 RDKRKRDLVL1390 NVWDFAGREE1400 FYSTHPHFMT 1410 QRALYLAVYD1420 LSKGQAEVDA1430 MKPWLFNIKA1440 RASSSPVILV1450 GTHLDVSKAC 1465 MSKITKELLN1475 KRGFPAIRDY1485 HFVNATEESD1495 ALAKLRKTII1505 NESLNFKIRD 1515 QLVVGQLIPD1525 CYVELEKIIL1535 SERKNVPIEF1545 PVIDRKRLLQ1555 LVRENQLQLD 1565 ENELPHAVHF1575 LNESGVLLHF1585 QDPALQLSDL1595 YFVEPKWLCK1605 IMAQILTVKV 1615 EGCPKHPKGI1625 ISRRDPKNYM1646 TQYFKLLEKF1656 QIALVPSSLS1674 DHRPVIELPH 1684 CENSEIIIRL1694 YEMPYFPMGF1704 WSRLINRLLE1714 ISPYMLALRP1729 NRMYWRQGIY 1739 LNWSPEAYCL1749 VGSEVLDNHP1759 ESFLKITVPS1769 CRKGCILLGQ1779 VVDHIDSLME 1789 EWFPGLLEID1799 ICGEGETLLK1809 KWALYSFNDG1819 EEHQKILLDD1829 LMKKAEEGDL 1839 LVNPDQPRLT1849 IPISQIAPDL1859 ILADLPRNIM1869 LNNDELEFEQ1879 APEFLLGDGS 1889 FGSVYRAAYE1899 GEEVAVKIFN1909 KHTSLRLLRQ1919 ELVVLCHLHH1929 PSLISLLAAG 1939 IRPRMLVMEL1949 ASKGSLDRLL1959 QQDKASLTRT1969 LQHRIALHVA1979 DGLRYLHSAM 1989 IIYRDLKPHN1999 VLLFTLYPNA2009 AIIAKIADYS2019 IAQYCCRMTS2032 EGTPGFRAPE 2042 VARGNVIYNQ2052 QADVYSFGLL2062 LYDILTTGGR2072 IVEGLKFPNE2082 FDELEIQGKL 2092 PDPVKEYGCA2102 PWPMVEKLIK2112 QCLKENPQER2122 PTSAQVFDIL2132 NSAELVCLTR 2142 RILLPKNVIV2152 ECMVATHHNS2162 RNASIWLGCG2172 HTDRGQLSFL2182 DLNTEGYTSE 2192 EVADSRILCL2202 ALVHLPVEKE2212 SWIVSGTQSG2222 TLLVINTEDG2232 KKRHTLEKMT 2242 DSVTCLYCNS2252 FSKQSKQKNF2262 LLVGTADGKL2272 AIFEDKTVKL2282 KGAAPLKILN 2292 IGNVSTPLMC2302 LSESTNSTER2312 NVMWGGCGTK2322 IFSFSNDFTI2332 QKLIETRTSQ 2342 LFSYAAFSDS2352 NIITVVVDTA2362 LYIAKQNSPV2372 VEVWDKKTEK2382 LCGLIDCVHF 2392 LREVTVKENK2402 ESKHKMSYSG2412 RVKTLCLQKN2422 TALWIGTGGG2432 HILLLDLSTR 2442 RLIRVIYNFC2452 NSVRVMMTAQ2462 LGSLKNVMLV2472 LGYNRKNTEG2482 TQKQKEIQSC 2492 LTVWDINLPH2502 EVQNLEKHIE2512 VRKELAEKMR2522 RTSVE
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1343 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1364 or .A:1365 or .A:1366 or .A:1367 or .A:1368 or .A:1395 or .A:1396 or .A:1397 or .A:1398 or .A:1452 or .A:1453 or .A:1455 or .A:1489 or .A:1490 or .A:1491; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
THR1343
3.874
GLY1344
3.342
SER1345
2.683
GLY1346
3.946
LYS1347
3.077
THR1348
3.185
THR1349
3.189
MET1364
3.848
GLN1365
3.499
SER1366
4.713
ALA1367
4.274
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| PDB ID: 6VP6 Cryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) | ||||||
| Method | Electron microscopy | Resolution | 3.47 Å | Mutation | No | [2] |
| PDB Sequence |
VPYNRMKLMI
1339 VGNGSGKTTL1350 LQQLMGIDVK1374 DWPILVLNVW1393 DFAGREEFYS1403 THPRALYLAV 1418 YDLSKGQAEV1428 DAMKPWLFNI1438 KARASSSPVI1448 LVGTHLDVSD1458 EKQRKACMSK 1468 ITKELLNKRG1478 FPAIRDYHFV1488 NATEESDALA1498 KLRKTIINES1508 LNFKIRDQLV 1518 VGQLIPDCYV1528 ELEKIILSER1538 KNVPIEFPVI1548 DRKRLLQLVR1558 ENQLQLDENE 1568 LPHAVHFLNE1578 SGVLLHFQAL1590 QLSDLYFVEP1600 KWLCKIMAQI1610 LTVGIISRRD 1630 VEKFLSKKRK1640 FPKNYMSQYF1650 KLLEKFQIAL1660 PIGEEYLLVP1670 SSLSDHRPVI 1680 ELPHCENSEI1690 IIRLYEMPYF1700 PMGFWSRLIN1710 RLLEISPYML1720 LRPNRMYWRQ 1736 GIYLNWSPEA1746 YCLVGSEVLD1756 NHPESFLKIT1766 VPSCRKGCIL1776 LGQVVDHIDS 1786 LMEEWFPGLL1796 LLKKWALYSF1816 NDGEEHQKIL1826 LDDLMKKAEE1836 GDLLVNPDQP 1846 RLTIPISQIA1856 PDLILADLPR1866 NIMLNNDELE1876 FEQAPEFLLG1886 DGSFGSVYRA 1896 AYEGEEVAVK1906 IFNKHTSLRL1916 LRQELVVLCH1926 LHHPSLISLL1936 AAGIRPRMLV 1946 MELASKGSLD1956 RLLQQDKASL1966 TRTLQHRIAL1976 HVADGLRYLH1986 SAMIIYRDLK 1996 PHNVLLFTLY2006 PNAAIIAKIA2016 DYGPGFRAPE2042 VARGNVIYNQ2052 QADVYSFGLL 2062 LYDILTTGGR2072 IVEGLKFPNE2082 FDELEIQGKL2092 PDPVKEYGCA2102 PWPMVEKLIK 2112 QCLKENPQER2122 PTSAQVFDIL2132 NSAELVCLTR2142 RILLPKNVIV2152 ECMVATHHAS 2166 IWLGCGHTDR2176 GQLSFLDLNT2186 EGYTSEEVAD2196 SRILCLALVH2206 LPVEKESWIV 2216 SGTQSGTLLV2226 INTEDGKKRH2236 TLEKMTDSVT2246 CLYCNFLLVG2266 TADGKLAIFE 2276 DKTVKLKGAA2286 PLKILNIGNV2296 STPLMCLSES2306 NVMWGGCGTK2322 IFSFSNDFTI 2332 QKLIETRTSQ2342 LFSYAAFSDS2352 NIITVVVDTA2362 LYIAKQNSPV2372 VEVWDKKTEK 2382 LCGLIDCVHF2392 LREVMMSYSG2412 RVKTLCLQKN2422 TALWIGTGGG2432 HILLLDLSTR 2442 RLIRVIYNFC2452 NSVRVMMTAQ2462 LGSLKNVMLV2472 LGYNREIQSC2492 LTVWDINLPH 2502 EVQNLEKHIE2512 VRKELAEKMR2522 RTS
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1396 or .A:1453 or .A:1455 or .A:1456 or .A:1488 or .A:1489 or .A:1490 or .A:1491; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6VNO Cryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) | ||||||
| Method | Electron microscopy | Resolution | 3.50 Å | Mutation | No | [2] |
| PDB Sequence |
VPYNRMKLMI
1339 VGNGSGKTTL1350 LQQLMGIDVK1374 DWPILVLNVW1393 DFAGREEFYS1403 THPRALYLAV 1418 YDLSKGQAEV1428 DAMKPWLFNI1438 KARASSSPVI1448 LVGTHLDVSD1458 EKQRKACMSK 1468 ITKELLNKRG1478 FPAIRDYHFV1488 NATEESDALA1498 KLRKTIINES1508 LNFKIRDQLV 1518 VGQLIPDCYV1528 ELEKIILSER1538 KNVPIEFPVI1548 DRKRLLQLVR1558 ENQLQLDENE 1568 LPHAVHFLNE1578 SGVLLHFQAL1590 QLSDLYFVEP1600 KWLCKIMAQI1610 LTVGIISRRD 1630 VEKFLSKKRK1640 FPKNYMSQYF1650 KLLEKFQIAL1660 PIGEEYLLVP1670 SSLSDHRPVI 1680 ELPHCENSEI1690 IIRLYEMPYF1700 PMGFWSRLIN1710 RLLEISPYML1720 LRPNRMYWRQ 1736 GIYLNWSPEA1746 YCLVGSEVLD1756 NHPESFLKIT1766 VPSCRKGCIL1776 LGQVVDHIDS 1786 LMEEWFPGLL1796 LLKKWALYSF1816 NDGEEHQKIL1826 LDDLMKKAEE1836 GDLLVNPDQP 1846 RLTIPISQIA1856 PDLILADLPR1866 NIMLNNDELE1876 FEQAPEFLLG1886 DGSFGSVYRA 1896 AYEGEEVAVK1906 IFNKHTSLRL1916 LRQELVVLCH1926 LHHPSLISLL1936 AAGIRPRMLV 1946 MELASKGSLD1956 RLLQQDKASL1966 TRTLQHRIAL1976 HVADGLRYLH1986 SAMIIYRDLK 1996 PHNVLLFTLY2006 PNAAIIAKIA2016 DYGPGFRAPE2042 VARGNVIYNQ2052 QADVYSFGLL 2062 LYDILTTGGR2072 IVEGLKFPNE2082 FDELEIQGKL2092 PDPVKEYGCA2102 PWPMVEKLIK 2112 QCLKENPQER2122 PTSAQVFDIL2132 NSAELVCLTR2142 RILLPKNVIV2152 ECMVATHHAS 2166 IWLGCGHTDR2176 GQLSFLDLNT2186 EGYTSEEVAD2196 SRILCLALVH2206 LPVEKESWIV 2216 SGTQSGTLLV2226 INTEDGKKRH2236 TLEKMTDSVT2246 CLYCNFLLVG2266 TADGKLAIFE 2276 DKTVKLKGAA2286 PLKILNIGNV2296 STPLMCLSES2306 NVMWGGCGTK2322 IFSFSNDFTI 2332 QKLIETRTSQ2342 LFSYAAFSDS2352 NIITVVVDTA2362 LYIAKQNSPV2372 VEVWDKKTEK 2382 LCGLIDCVHF2392 LREVMMSYSG2412 RVKTLCLQKN2422 TALWIGTGGG2432 HILLLDLSTR 2442 RLIRVIYNFC2452 NSVRVMMTAQ2462 LGSLKNVMLV2472 LGYNREIQSC2492 LTVWDINLPH 2502 EVQNLEKHIE2512 VRKELAEKMR2522 RTS
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1396 or .A:1453 or .A:1455 or .A:1456 or .A:1488 or .A:1489 or .A:1490 or .A:1491; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6OJF Dimeric structure of LRRK2 GTPase domain | ||||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | Yes | [3] |
| PDB Sequence |
YNRMKLMIVG
1341 NTGSGKTTLL1351 QQLMKTKKSD1361 LGMQSATVGI1371 DVKDWPIQIR1381 DKRKRDLVLN 1391 VWDFAGREEF1401 YSTHPHFMTQ1411 RALYLAVYDL1421 SKGQAEVDAM1431 KPWLFNIKAR 1441 ASSSPVILVG1451 THLDVSDEAQ1461 RAACMSKITK1471 ELLNKRGFPA1481 IRDYHFVNAT 1491 EESDALAKLR1501 KTIINESLNF1511 KIRDQLVV
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1343 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1350 or .A:1452 or .A:1453 or .A:1454 or .A:1455 or .A:1456 or .A:1488 or .A:1489 or .A:1490 or .A:1491; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6OJE Dimeric structure of LRRK2 GTPase domain | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [4] |
| PDB Sequence |
NRMKLMIVGN
1342 TGSGKTTLLQ1352 QLMKTKKSDL1362 GMQSATVGID1372 VKDWPIQIRD1382 KRKRDLVLNV 1392 WDFAGREEFY1402 STHPHFMTQR1412 ALYLAVYDLS1422 KGQAEVDAMK1432 PWLFNIKARA 1442 SSSPVILVGT1452 HLDVSDEKQR1462 KACMSKITKE1472 LLNKRGFPAI1482 RDYHFVNATE 1492 ESDALAKLRK1502 TIINESLNFK1512 IRDQLV
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1343 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1350 or .A:1452 or .A:1453 or .A:1454 or .A:1455 or .A:1456 or .A:1488 or .A:1489 or .A:1490 or .A:1491; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6XAF 1.9A crystal structure of the GTPase domain of Parkinson's disease-associated protein LRRK2 carrying R1398H | ||||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | Yes | [5] |
| PDB Sequence |
MKLMIVGNTG
1344 SGKTTLLQQL1354 MKQSATVGID1372 VKDWPIQIRD1382 KRKRDLVLNV1392 WDFAGHEEFY 1402 STHPHFMTQR1412 ALYLAVYDLS1422 KGQAEVDAMK1432 PWLFNIKARA1442 SSSPVILVGT 1452 HLDVSDEAQR1462 AACMSKITKE1472 LLNKRGFPAI1482 RDYHFVNATE1492 ESDALAKLRK 1502 TIINESLNFK1512 IR
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1343 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1350 or .A:1452 or .A:1453 or .A:1454 or .A:1455 or .A:1456 or .A:1488 or .A:1489 or .A:1490 or .A:1491; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2ZEJ Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [6] |
| PDB Sequence |
KLIVGNTGSG
1346 KTTLLQQLKT1368 VGIDVKDWPI1378 LVLNVWDFAG1397 REEFYSTHPH1407 FTQRALYLAV 1418 YDLSKGQAEV1428 DAKPWLFNIK1439 ARASSSPVIL1449 VGTHLDVSDE1459 KQRKACSKIT 1470 KELLNKRGFP1480 AIRDYHFVNA1490 TEESDALAKL1500 RKTIINESLN1510 F |
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .A:1342 or .A:1343 or .A:1344 or .A:1345 or .A:1346 or .A:1347 or .A:1348 or .A:1349 or .A:1350 or .A:1368 or .A:1394 or .A:1396; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3D6T Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase | ||||||
| Method | X-ray diffraction | Resolution | 2.43 Å | Mutation | No | [6] |
| PDB Sequence |
KLIVGNTGSG
1346 KTTLLQLGID1372 VKDWPLVLVW1393 DFAGREEFYS1403 THPHFTQRAL1414 YLAVYDLSKG 1424 QAEVDAKPWL1435 FNIKARASSS1445 PVILVGTHLD1455 VSDKILLGFP1480 AIRDYHFVNA 1490 TEESLRKTII1505
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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 .GDP or .GDP2 or .GDP3 or :3GDP;style chemicals stick;color identity;select .B:1452 or .B:1453 or .B:1454 or .B:1455 or .B:1456 or .B:1488 or .B:1489 or .B:1490 or .B:1491; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural analysis of the full-length human LRRK2. Cell. 2021 Jun 24;184(13):3519-3527.e10. | ||||
| REF 2 | Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature. 2020 Dec;588(7837):344-349. | ||||
| REF 3 | Structural basis for conformational plasticity in the GTPase domain of the Parkinson's disease-associated protein LRRK2 | ||||
| REF 4 | Structural basis for conformational plasticity in the GTPase domain of the Parkinson's disease-associated protein LRRK2 | ||||
| REF 5 | Structural basis for conformational plasticity in the GTPase domain of the Parkinson's disease-associated protein LRRK2 | ||||
| REF 6 | Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase. Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1499-504. | ||||
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