Structure of PDB 8ptk Chain n Binding Site BS01

Receptor Information

>8ptk Chain n (length=4566) Species: 9606 (Homo sapiens)

AVQNVADVSVLQKHLRKLVPLLLEDGGEAPAALEAALEEKSALEQMRKFL
SDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNINIDIHYGVKSNSLAFI
KRTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKSYIRESG
KADRDGDKMAPSVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQ
CYERGEKPKVTDFGDKVEDPTFLNQLQSGVNRWIREIQKVTKLDRDPASG
TALQEISFWLNLERALYRIQEKRESPEVLLTLDILKHGKRFHATVSFDTD
TGLKQALETVNDYNPLMKDFPLNDLLSATELDKIRQALVAIFTHLRKIRN
TKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMHVAYEEFEKVMVACFEV
FQTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARLDQMRKF
RRQHEQLRAVIVRVLRPQVFDAADANAIEEVNLAYENVKEVDGLDVSKEG
TEAWEAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALF
VRPHIRGAIREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLP
PVSGSIIWAKQIDRQLTAYMKRVEDVLGKGWENHVEGQKLKQDGDSFRMK
LNTQEIFDDWARKVQQRNLGVSGRIFTIKLKVNFLPEIITLSKEVRNLKW
LGFRVPLAIVNKAHQANQLYPFAISLIESVRTYERTCEKVEERNTISLLV
AGLKKEVQALIAEGIALVWESYKLDPYVQRLAETVFNFQEKVDDLLIIEE
KIDLEVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIWVNKLDM
EIERILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAPQVSHKPGGEPKI
KNVVHELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQRYQ
VGVHYELTEEEKFYRNALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWL
QYQCLWDMQAENIYNRLGEDLNKWQALLVQIRKARGTFDNAETKKEFGPV
VIDYGKVQSKVNLKYDSWHKEVLSKFGQMLGSNMTEFHSQISKSRQELEQ
HSVDTASTSDAVTFITYVQSLKRKIKQFEKQVELYRNGQRLLEKQRFQFP
PSWLYIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKIVQEDRAVESRTT
DLLTDWEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEALE
LTDTGLLSGSEERVQVALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQ
PRKLRQNLDALLNQLKSFPARLRQYASYEFVQRLLKGYMKINMLVIELKS
EALKDRHWKQLMKRLHVNWVVSELTLGQIWDVDLQKNEAIVKDVLLVAQG
EMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVS
AMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSA
DIKHLLPVETQEFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLA
DLLGEIQKALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFK
KMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLV
EKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQ
IAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRR
RKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQ
QLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPF
GPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWG
CFDEFNRLEERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQ
VKVSPDMAIFITMNPGSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGF
RTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQ
KIKREKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFS
LLSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQ
LYQITQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAI
SKDHLYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDP
EWVENLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRC
GMVWFSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKGKEDEGEEAA
SPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLF
SMLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLK
MRAELGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVET
HKVAAPDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSAL
RALPDMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWL
VLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFV
GACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLI
PSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEA
LRPLETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFP
NIDREKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEELDVPL
VLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNGLSVY
QIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGFLERMN
TLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVI
RNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEF
TSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANA
RLAKRGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVGLRKIK
ETVDQVEELRRDLRIKSQELEVKNAAANDKLKKMVKDQQEAEKKKVMSQE
IQEQLHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKSIKKQHLVEVRS
MANPPAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEEI
SDAIREKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRV
EPLRNELQKLEDDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQ
AIKADLAAVEAKVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLL
SAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADER
LRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKI
TRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGR
VLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQ
SQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGR
ILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACS
SIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSII
TKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFL
RGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGI
WLDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFV
STNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLA
AEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQL
EKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLR
TFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGE
SDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNE
FDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWV
ELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDAWMRTL
HTTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQD
LADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVS
DFSERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQ
ANSWSLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNA
ISTALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKE
DPRSFYERGVAVLCTE

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8ptk Chain n Residue 4701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ptk Molecular mechanism of dynein-dynactin complex assembly by LIS1
• Resolution: 10.0 Å
• Binding residue (original residue number in PDB): V1880 A1908 G1909 T1910 G1911 K1912
• Binding residue (residue number reindexed from 1): V1825 A1853 G1854 T1855 G1856 K1857
• Annotation score: 5

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

External links

• PDB: RCSB:8ptk, PDBe:8ptk, PDBj:8ptk
• PDBsum: 8ptk
• PubMed: 38547289
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)