Structure of PDB 8fd6 Chain A Binding Site BS01

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 IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8fd6 Chain A Residue 3201 [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)		L736 T737 W748 G772 S773 G774 K775 M777 E889 L914 M918 N922 R1271
Binding residue
(residue number reindexed from 1)		L592 T593 W604 G628 S629 G630 K631 M633 E745 L770 M774 N778 R1105
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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