Structure of PDB 8fdt Chain A Binding Site BS04

Receptor Information
>8fdt Chain A (length=2736) Species: 9606,300852 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RWVYLEGIFTGSADIKHLLPVETQRFQLLGKIQKALGEYLERERSSFPRF
YFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSR
EGEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGK
ATSIDPNTYITWIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLH
SVLSNVEVTLNVLADSVLMEQPPLRRRKLEHLITELVHQRDVTRSLIKSK
IDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMANAKFNYGFEYLGVQDKL
VQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALGHQLGRFVLV
FNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQ
EALREHSNPITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFR
SLAMTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYD
FGLRALKSVLVSAGNVKRERIQKIKREIAENLPEQEILIQSVCETMVPKL
VAEDIPLLFSLLSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEV
GGMWVEKVLQLYQITQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEG
VAHIIDPKAISKDHLYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQ
WIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLK
YATLATVSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLSPMLQIQRDAAT
IMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQ
YNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRRI
TTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPT
LDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLN
FSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDM
DKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFVGACNPPTDPGRK
PLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTA
AMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEGL
IRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPI
LYSNWLSKDYIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLR
IDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGED
FDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGFLERMNTLLANGEVPGLF
EGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLHVVFTMNPS
SEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNYI
VPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAI
TPRHYLDFINHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRK
VNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFD
QQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQASSLPADD
LCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFRK
NLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDIDL
SPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAER
PDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTLE
NLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQI
HFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKDLFQVAFNRV
ARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNEIVLSAGST
PRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVP
YLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIM
EQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAI
GSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHAC
FRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICK
SPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDT
WLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLER
LFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWL
GLPNNAERVLLTTQGVDMISKMLKMQAWMRTLHTTASNWLHLIPQTLSHL
KRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYL
RTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAAS
GGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTFG
VTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTEKKASVVTLPV
YLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLCT
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 chain8fdt Chain A Residue 3204 [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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PDB8fdt Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		L424 V425 G454 T455 G456 K457 T458 E459 I594 L635 R636 K639 D866
Binding residue
(residue number reindexed from 1)		L300 V301 G330 T331 G332 K333 T334 E335 I462 L503 R504 K507 D722
Annotation score5
Enzymatic activity
Enzyme Commision number 6.1.1.11: serine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide 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
Cellular Component
GO:0030286 dynein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fdt, PDBe:8fdt, PDBj:8fdt
PDBsum8fdt
PubMed37322240
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1);
Q5SJX7

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