Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Adenosine triphosphate | Ligand Info | |||||
| Structure Description | Structure of LRRK2 after symmetry expansion | PDB:7LI4 | ||||
| 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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| Ligand Name: Phosphonothreonine | Ligand Info | |||||
| Structure Description | Cryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) | PDB:6VP6 | ||||
| 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 View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Guanosine-5'-Diphosphate | Ligand Info | |||||
| Structure Description | Dimeric structure of LRRK2 GTPase domain | PDB:6OJF | ||||
| 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase | PDB:2ZEJ | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| 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 .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:1336 or .A:1337 or .A:1339 or .A:1340 or .A:1350 or .A:1351 or .A:1352 or .A:1353 or .A:1354 or .A:1356 or .A:1374 or .A:1375 or .A:1376 or .A:1377 or .A:1389 or .A:1390 or .A:1391 or .A:1393 or .A:1395 or .A:1401 or .A:1403 or .A:1404 or .A:1405 or .A:1406 or .A:1407 or .A:1408 or .A:1410 or .A:1411 or .A:1412 or .A:1413 or .A:1415 or .A:1417 or .A:1418 or .A:1419 or .A:1427 or .A:1428 or .A:1429 or .A:1430 or .A:1432 or .A:1433 or .A:1434 or .A:1435 or .A:1449 or .A:1461 or .A:1462 or .A:1463 or .A:1464 or .A:1465 or .A:1467 or .A:1468 or .A:1469 or .A:1470 or .A:1471 or .A:1473 or .A:1485 or .A:1487; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LYS1336
1.340
LEU1337
1.326
ILE1339
1.336
VAL1340
3.814
LEU1350
4.983
LEU1351
2.828
GLN1352
3.354
GLN1353
3.265
LEU1354
1.306
LYS1356
1.322
LYS1374
4.421
ASP1375
3.471
TRP1376
3.544
PRO1377
4.955
VAL1389
4.271
LEU1390
3.542
ASN1391
2.800
TRP1393
3.500
PHE1395
4.013
PHE1401
3.842
SER1403
4.093
THR1404
3.241
HIS1405
3.130
PRO1406
3.282
HIS1407
3.315
PHE1408
1.326
THR1410
1.327
GLN1411
3.758
ARG1412
4.879
ALA1413
4.011
TYR1415
4.521
ALA1417
3.987
VAL1418
3.877
TYR1419
3.962
GLU1427
3.235
VAL1428
3.053
ASP1429
3.003
ALA1430
1.333
LYS1432
1.338
PRO1433
3.411
TRP1434
3.124
LEU1435
2.945
LEU1449
4.519
GLN1461
4.828
ARG1462
3.083
LYS1463
3.491
ALA1464
3.248
CYS1465
1.325
SER1467
1.340
LYS1468
3.309
ILE1469
3.291
THR1470
2.760
LYS1471
4.782
LEU1473
4.349
TYR1485
3.890
PHE1487
4.070
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| 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 | 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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