Structure of PDB 8fd6 Chain A Binding Site BS03

Receptor Information
>8fd6 Chain A (length=2747) 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
GGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTTS
QGATLDACSFGVTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNT
EKKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLCT
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 chain8fd6 Chain A Residue 3203 [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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PDB8fd6 Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		V1452 V1455 S1484 G1485 G1487 K1488 T1489 T1490 W1642 L1722
Binding residue
(residue number reindexed from 1)		V1286 V1289 S1318 G1319 G1321 K1322 T1323 T1324 W1476 L1556
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:8fd6, PDBe:8fd6, PDBj:8fd6
PDBsum8fd6
PubMed37322240
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1);
Q5SJX7

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