Structure of PDB 6sc2 Chain B Binding Site BS03

Receptor Information
>6sc2 Chain B (length=3930) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLFIFTTTQNYFGLMSELWDQPLLCNCLEINNFLDDGNQMLLRVQRSDAG
ISFSNTIEFGDTKDKVLVFFKLRPEVITDENLHDNILVSSMLESPISSLY
QAVRQVFAPMLLKDQEWSRNFDPKLQNLLSELEAGLGIVLRRSKERANYF
KELFETIAREFYNLDSLSLLEVVDLVETTQDVVDDVWRQTEHDHYPESRM
LHLLDIIGGSFGRFVQKKLGTLNLWEDPYYLVKESLKAGISICEQWVIVC
NHLTGQVWQRYVPHPWKNEKYFPETLDKLGKRLEEVLAIRTIHEKFLYFL
PASEEKIICLTRVFEPFTGLNPVQYNPYTEPLWKAAVSQYEKIIAPAEQK
IAGKLKNYISEIQDSPQQLLQAFLKYKELVKRPTISKELMLERETLLARL
VDSIKDFRLDFENRCRGIPGDASGPLSGKNLSEVVNSIVWVRQLELKVDD
TIKIAEALLSDLPGFRCFHQSAKDLLDQLKLYEQEQFDDWSRDIQSGLSD
SRSGLCIEASSRIMELDSNDGLLKVHYSDRLVILLREVRQLSALGFVIPA
KIQQVANIAQKFCKQAIILKQVAHFYNSIDQQMIQSQRPMMLQSALAFEQ
IIKNSKAGSGGKSQITWDNPKELEGYIQKLQNAAERLATENRKLRKWHTT
FCEKVVVLMNIDLLRQQQRWKDGLQELRTGLATVEAQGFQASDMHAWKQH
WNHQLYKALEHQYQMGLEALNENLPEINIDLTYKQGRLQFRPPFEEIRAK
YYREMKRFIGIPNQFKGVGEAGDESIFSIMIDRNASGFLTIFSKAEDLFR
RLSAVLHQHKEWIVIGQVDMEALVEKHLFTVHDWEKNFKALKIKGKEVER
LPSAVKVDCLNINCNPVKTVIDDLIQKAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AATLIDYEDSQSRTMKLIKDWKDIVNQVGDNRCLLQSLKDSPYYKGFEDK
VSIWERKLAELDEYLQNLNHIQRKWVYLEPIFGRGALPKEQTRFNRVDED
FRSIMTDIKKDNRVTTLTTHAGIRNSLLTILDQLQRCQRSLNEFLEEKRS
AFPRFYFIGDDDLLEILGQSTNPSVIQSHLKKLFAGINSVCFDEKSKHIT
AMKSLEGEVVPFKNKVPLSNNVETWLNDLALEMKKTLEQLLKECVTTGRS
SQGAVDPSLFPSQILCLAEQIKFTEDVENAIKDHSLHQIETQLVNKLEQY
TNIDTSSEDPGNTESGILELKLKALILDIIHNIDVVKQLNQIQVHTTEDW
AWKKQLRFYMKSDHTCCVQMVDSEFQYTYEYQGNASKLVYTPLTDKCYLT
LTQAMKMGLGGNPYGPAGTGKTESVKALGGLLGRQVLVFNCDEGIDVKSM
GRIFVGLVKCGAWGCFDEFNRLEESVLSAVSMQIQTIQDALKNHRTVCEL
LGKEVEVNSNSGIFITMNPAGKGYGGRQKLPDNLKQLFRPVAMSHPDNEL
IAEVILYSEGFKDAKVLSRKLVAIFNLSRELLTPQQHYDWGLRALKTVLR
GSGNLLRQLNKSGTTQNANESHIVVQALRLNTMSKFTFTDCTRFDALIKD
VFPGIELKEVEYDELSAALKQVFEEANYEIIPNQIKKALELYEQLCQRMG
VVIVGPSGAGKSTLWRMLRAALCKTGKVVKQYTMNPKAMPRYQLLGHIDM
DTREWSDGVLTNSARQVVREPQDVSSWIICDGDIDPEWIESLNSVLDDNR
LLTMPSGERIQFGPNVNFVFETHDLSCASPATISRMGMIFLSDEETDLNS
LIKSWLRNQPAEYRNNLENWIGDYFEKALQWVLKQNDYVVETSLVGTVMN
GLSHLHGCRDHDEFIINLIRGLGGNLNMKSRLEFTKEVFHWARESPPDFH
KPMDTYYDSTRGRLATYVLKKPEDLTADDFSNGLTLPVIQTPDMQRGLDY
FKPWLSSDTKQPFILVGPEGCGKGMLLRYAFSQLRSTQIATVHCSAQTTS
RHLLQKLSQTCMVISTNTGRVYRPKDCERLVLYLKDINLPKLDKWGTSTL
VAFLQQVLTYQGFYDENLEWVGLENIQIVASMSAGGRLGRHKLTTRFTSI
VRLCSIDYPEREQLQTIYGAYLEPVLHKNLKNHSIWGSSSKIYLLAGSMV
QVYEQVRAKFTVDDYSHYFFTPCILTQWVLGLFRYDLEGGSSNHPLDYVL
EIVAYEARRLFRDKIVGAKELHLFDIILTSVFQGDWGSDILDNMSDSFYV
TWGARHNSGAPGQPLPPHGKPLGKLNSTDLKDVIKKGLIHYGRDNQNLDI
LLFHEVLEYMSRIDRVLSFPGGSLLLAGRSGVGRRTITSLVSHMHGAVLF
SPKISRGYELKQFKNDLKHVLQLAGIEAQQVVLLLEDYQFVHPTFLEMIN
SLLSSGEVPGLYTLEELEPLLLPLKDQASQDGFFGPVFNYFTYRIQQNLH
IVLIMDSANSNFMINCESNPALHKKCQVLWMEGWSNSSMKKIPEMLFSEV
DPDFLKSFLLIHESCKAYGATPSQYMTFLHVYSAISSSKKKELLKRQSHL
QAGVSKLNEAKALVDELNRKAGEQSVLLETIKAAEVLINQLDREHKRWNA
QVVEITEELATLPKRAQLAAAFITYLSAAPESLRKTCLEEWTKSAGLEKF
DLRRFLCTESEQLIWKSEGLPSDDLSIENALVILQSRVCPFLIDPSSQAT
EWLKTHLKDSRLEVINQQDSNFITALELAVRFGKTLIIQEMDGVEPVLYP
LLRRDLVAQGPRYVVQIGDKIIDYNEEFRLFLSTRNPNPFIPPDAASIVT
EVNFTTTRSGLRGQLLALTIQHEKPDLEEQKTKLLQQEEDKKIQLAKLEE
SLLETLATSQGNILENKDLIESLNQTKASSALIQESLKESYKLQISLDQE
RDAYLPLAESASKMYFIISDLSKINNMYRFSLAAFLRLFQRALQNKQDSE
NTEQRIQSLISSLQHMVYEYICRCLFKADQLMFALHFVRGMHPELFQENE
WDTFTGVDQLPSWIDQERSWAVATLKIALPSLYQTLCFEDAALWRTYYNN
SMCEQEFPSILAKKVSLFQQILVVQVLRPDRLQSAMALFACKTLGLKEVS
PLPLNLKRLYKETLEIEPILIIISPGADPSQELQELANAERSGECYHQVA
MGQGQADLAIQMLKECARNGDWLCLKNLHLVVSWLPVLEKELNTLQPKDT
FRLWLTAEVHPNFTPILLQSSLKITYESPPGLKKNLMRTYESWTPEQISK
KDNTHRAHALFSLAWFHAACQERRNYIPQGWTKFYEFSLSDLRAGYNIID
RLFDGAKDVQWEFVHGLLENAIYGGRIDNYFDLRVLQSYLKQFFIFPYSV
SLPQSCSILDYRAVIEKIPEDDKPSFFGLPANIARSSQRMISSQVISQLR
ILGRDREIWSNELSPVLNLWKKLNQNSNLIHQKVPPPNDRQGSPILSFII
LEQFNAIRLVQSVHQSLAALSKVIRGTTLLSSEVQKLASALLNQKCPLAW
QSKWEGPEDPLQYLRGLVARALAIQNWVDKAEKQALLSETLDLSELFHPD
TFLNALRQETARAVGRSVDSLKFVASWKGRLQEAKLQIKISGLLLEGCSF
DGNQLSENQLDSPSVSSVLPCFMGWIPQDACGPYSPDECISLPVYTSAER
DRVVTNIDVPCGGNQDQWIQCGAALFLKNQ
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6sc2 Chain B Residue 4404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6sc2 Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		G2294 C2295 G2296 G2298
Binding residue
(residue number reindexed from 1)		G2220 C2221 G2222 G2224
Annotation score1
Enzymatic activity
Enzyme Commision number ?
2.1.1.63: methylated-DNA--[protein]-cysteine S-methyltransferase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity
GO:0005524 ATP binding
GO:0008168 methyltransferase activity
GO:0008569 minus-end-directed microtubule motor activity
GO:0016887 ATP hydrolysis activity
GO:0045505 dynein intermediate chain binding
GO:0046872 metal ion binding
GO:0051959 dynein light intermediate chain binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0007018 microtubule-based movement
GO:0030030 cell projection organization
GO:0032259 methylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0030286 dynein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6sc2, PDBe:6sc2, PDBj:6sc2
PDBsum6sc2
PubMed31451806
UniProtB0I1S0;
E5BBQ0

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