Structure of PDB 8ptk Chain f Binding Site BS03

Receptor Information
>8ptk Chain f (length=4502) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVQNVADVSVLQKHLRKLVPLLLEDGGEAPAALEAALEEKSALEQMRKFL
SDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNINIDIHYGVKSNSLAFI
KRTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKSYIRESG
KADRDGDKMAPSVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQ
CYERGEKPKVTDFGDKVEDPTFLNQLQSGVNRWIREIQKVTKLDRDPASG
TALQEISFWLNLERALYRIQEKRESPEVLLTLDILKHGKRFHATVSFDTD
TGLKQALETVNDYNPLMKDFPLNDLLSATELDKIRQALVAIFTHLRKIRN
TKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMHVAYEEFEKVMVACFEV
FQTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARLDQMRKF
RRQHEQLRAVIVRVLRPQVFDAADANAIEEVNLAYENVKEVDGLDVSKEG
TEAWEAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALF
VRPHIRGAIREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLP
PVSGSIIWAKQIDRQLTAYMKRVEDVLGKGWENHVEGQKLKQDGDSFRMK
LNTQEIFDDWARKVQQRNLGVSGRIFTIESTRVRGRTGNVLKLKVNFLPE
IITLSKEVRNLKWLGFRVPLAIVNKAHQANQLYPFAISLIESVRTYERTC
EKVEERNTISLLVAGLKKEVQALIAEGIALVWESYKLDPYVQRLAETVFN
FQEKVDDLLIIEEKIDLEVRSLETCMYDHKTFSEILNRVQKAVDDLNLHS
YSNLPIWVNKLDMEIERILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDA
PQVSHKPGGEPKIKNVVHELRITNQVIYLNPPIEECRYKLYQEMFAWKMV
VLSLPRIQSQRYQVGVHYELTEEEKFYRNALTRMPDGPVALEESYSAVMG
IVSEVEQYVKVWLQYQCLWDMQAENIYNRLGEDLNKWQALLVQIRKARGT
FDNAETKKEFGPVVIDYGKVQSKVNLKYDSWHKEVLSKFGQMLGSNMTEF
HSQISKSRQELEQHSVDTASTSDAVTFITYVQSLKRKIKQFEKQVELYRN
GQRLLEKQRFQFPPSWLYIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMK
IVQEDRAVESRTTDLLTDWEKTKPVTGNLRPEEALQALTIYEGKFGRLKD
DREKCAKAKEALELTDTGLLSGSEERVQVALEELQDLKGVWSELSKVWEQ
IDQMKEQPWVSVQPRKLRQNLDALLNQLKSFPARLRQYASYEFVQRLLKG
YMKINMLVIELKSEALKDRHWKQLMKRLHVNWVVSELTLGQIWDVDLQKN
EAIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDD
LFNKVKEHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQR
RWVYLEGIFTGSADIKHLLPVETQEFQSISTEFLALMKKVSKSPLVMDVL
NIQGVQRSLERLADLLGEIQKALGEYLERERSSFPRFYFVGDEDLLEIIG
NSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSI
TEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWI
DKYQAQLVVLSAQIAWSENVETALSSAAPLHSVLSNVEVTLNVLADSVLM
EQPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDP
KQTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEA
RLGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGL
CQVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNPITCELLNKQV
KVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYS
QGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRE
RIQKIKREAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQ
YHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHG
LMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLD
PNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVL
DDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVL
STDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQPYFTSNGLVTKALE
HAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLER
YIQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYE
VSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEH
KPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHY
CEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVE
HGGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDY
PGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDT
QPHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLV
EDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEE
LRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGV
SGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNE
KIAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQ
KEGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNR
CVLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPS
HREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFH
EKRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAAND
KLKKMVKDQQEAEKKKVMSQEIQEQLHKQQEVIADKQMSVKEDLDKVEPA
VIEAQNAVKSIKKQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQI
RSIIMRENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNYEIVNRASLA
CGPMVKWAIAQLNYADMLKRVEPLRNELQKLEDDAKDNQQKANEVEQMIR
DLEASIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTALLKSLSAERER
WEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQ
ANIQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPL
IIDPSGQATEFIMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDV
ESYDPVLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEF
PPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEF
QLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEETD
IVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHN
VLYENPNLVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARI
KLKGTGEPTYDAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCL
PAFKDLIAKVQADEQFGIWLDSSSPEQTVPYLWTPATPIGQAIHRLLLIQ
AFRPDRLLAMAHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMC
SVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWV
MLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRI
FVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERL
RYAPLGWSKKYEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALK
TLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDI
QMPDGIRREEFVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKML
KMQMLETLHTTASNWLHLIPQTLSHLKRTENIKDPLFRFFEREVKMGAKL
LQDVRQDLADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGM
TVIQWVSDFSERIKQLQNISLAAASKELKNIHVCLGGLFVPEAYITATRQ
YVAQANSWSLEELCLEVNVSFGVTGLKLQGATCNNNKLSLSNAISTALPL
TQLRWVKQSVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLC
TE
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 chain8ptk Chain f Residue 4805 [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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PDB8ptk Molecular mechanism of dynein-dynactin complex assembly by LIS1
Resolution10.0 Å
Binding residue
(original residue number in PDB)		V2569 G2598 K2601 T2602
Binding residue
(residue number reindexed from 1)		V2481 G2510 K2513 T2514
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008569 minus-end-directed microtubule motor activity
GO:0016887 ATP hydrolysis activity
GO:0045505 dynein intermediate chain binding
GO:0051959 dynein light intermediate chain binding
Biological Process
GO:0007018 microtubule-based movement
GO:0007052 mitotic spindle organization
GO:0007097 nuclear migration
GO:0008090 retrograde axonal transport
GO:0031122 cytoplasmic microtubule organization
GO:0032388 positive regulation of intracellular transport
GO:0033962 P-body assembly
GO:0034063 stress granule assembly
GO:0051293 establishment of spindle localization
GO:0051301 cell division
GO:0060236 regulation of mitotic spindle organization
GO:0090235 regulation of metaphase plate congression
GO:0120162 positive regulation of cold-induced thermogenesis
GO:1905832 positive regulation of spindle assembly
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005868 cytoplasmic dynein complex
GO:0005874 microtubule
GO:0005881 cytoplasmic microtubule
GO:0005938 cell cortex
GO:0016020 membrane
GO:0030175 filopodium
GO:0030286 dynein complex
GO:0035578 azurophil granule lumen
GO:0070062 extracellular exosome
GO:1904115 axon cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ptk, PDBe:8ptk, PDBj:8ptk
PDBsum8ptk
PubMed38547289
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)

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