Structure of PDB 8ptk Chain m Binding Site BS03

Receptor Information
>8ptk Chain m (length=4562) 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
RRQHEQLRAVIVRVLRDAADANAIEEVNLAYENVKEVDGLDVSKEGTEAW
EAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALFVRPH
IRGAIREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLPPVSG
SIIWAKQIDRQLTAYMKRVEDVLGKGWENHVEGQKLKQDGDSFRMKLNTQ
EIFDDWARKVQQRNLGVSGRIFTIKLKVNFLPEIITLSKEVRNLKWLGFR
VPLAIVNKAHQANQLYPFAISLIESVRTYERTCEKVEERNTISLLVAGLK
KEVQALIAEGIALVWESYKLDPYVQRLAETVFNFQEKVDDLLIIEEKIDL
EVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIWVNKLDMEIER
ILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAPQVSHKPGGEPKIKNVV
HELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQRYQVGVH
YELTEEEKFYRNALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWLQYQC
LWDMQAENIYNRLGEDLNKWQALLVQIRKARGTFDNAETKKEFGPVVIDY
GKVQSKVNLKYDSWHKEVLSKFGQMLGSNMTEFHSQISKSRQELEQHSVD
TASTSDAVTFITYVQSLKRKIKQFEKQVELYRNGQRLLEKQRFQFPPSWL
YIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKIVQEDRAVESRTTDLLT
DWEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEALELTDT
GLLSGSEERVQVALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKL
RQNLDALLNQLKSFPARLRQYASYEFVQRLLKGYMKINMLVIELKSEALK
DRHWKQLMKRLHVNWVVSELTLGQIWDVDLQKNEAIVKDVLLVAQGEMAL
EEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKL
SPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKH
LLPVETQEFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLG
EIQKALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFA
GVSSIILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLVEKEM
RVTLAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWS
ENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLE
HLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSI
QMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAG
TGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDE
FNRLEERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQVKVS
PDMAIFITMNPGSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAE
VLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQKIKR
EKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSD
VFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQI
TQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDH
LYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVE
NLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVW
FSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKGKEDEGEEAASPML
QIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLH
QACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAE
LGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVA
APDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALP
DMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFC
DEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFVGACN
PPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLR
TYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPL
ETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDR
EKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEELDVPLVLFN
EVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKV
HRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGFLERMNTLLA
NGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLH
VVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKM
DLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAK
RGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVGLRKIKETVD
QVEELRRDLRIKSQELEVKNAAANDKLKKMVKDQQEAEKKKVMSQEIQEQ
LHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKSIKKQHLVEVRSMANP
PAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEEISDAI
REKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLR
NELQKLEDDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKA
DLAAVEAKVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAF
IAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQ
ASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTS
FLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLIT
LGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCL
NEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDD
DTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYF
TMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKDL
FQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNE
IVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDS
SSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNL
GESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQN
TQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKL
HSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSS
IPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLR
SACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQR
LLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLP
DTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDAWMRTLHTTA
SNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADV
VQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSE
RIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSW
SLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAISTA
LPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRS
FYERGVAVLCTE
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain8ptk Chain m Residue 4704 [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 G2600 K2601 T2602 M2603
Binding residue
(residue number reindexed from 1)		V2506 G2535 G2537 K2538 T2539 M2540
Annotation score3
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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