Structure of PDB 8dyv Chain A Binding Site BS02

Receptor Information
>8dyv Chain A (length=2549) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGISSREGEEVMFKTPLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNT
YITWIDKYQAQLVVLSAQIAWSENVETALSSAAPLHSVLSNVEVTLNVLA
DSVLMEQPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMR
FYFDPKQTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMT
QALEARLGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGR
IFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNITCELL
NKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQV
MLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGN
VKRERIQKIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGV
QYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINH
GLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTL
DPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSV
LDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDV
LSTDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQPYFTSNGLVTKAL
EHAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLE
RYIQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDY
EVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAE
HKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDH
YCEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMV
EHGGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVD
YPGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQD
TQPHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRL
VEDEERRWTDENIDTVALKHFPKAMSRPILYSNWLSKDYIPVDQEELRDY
VKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAG
KTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAF
IMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGL
MLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLN
WFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREA
IVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHEKRS
ELEEQQMHLNVGLRKIKETVDQNRSTALLKSLSAERERWEKTSETFKNQM
STIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIART
EYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFI
MNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLN
REVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVN
FTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLL
QALNILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLS
TACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNTDHTQRLSII
TKDLFQVAFNRVARGMLHQDHITFAMLLARIKLPTYDAEFQHFLRGNGLT
VEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYLWTPAT
PIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLDLTHIV
GTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQAD
KAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTMEIN
PKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYF
LLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTWLDDTAKGRQ
NISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSFDSE
FKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNNAERVL
LTTQGVDMISKMLKMQTLHTTASNWLHLIPQTLSHLKRIKDPLFRFFERE
VKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSH
YTVPAGMTVIQWVSDFSERIKQLQNISLAAASKELKNIHVCLGGLFVPEA
YITATRQYVAQANSWSLEELCLEVNVFGVTGLKLQGATCNNNKLSLLPLT
QLRWVKQSVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLC
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 chain8dyv Chain A Residue 4702 [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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PDB8dyv Structures of human dynein in complex with the lissencephaly 1 protein, LIS1.
Resolution3.97 Å
Binding residue
(original residue number in PDB)		G2598 S2599 G2600 T2602 M2603 P2739 I2747 R2797 T2800
Binding residue
(residue number reindexed from 1)		G861 S862 G863 T865 M866 P1002 I1010 R1060 T1063
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
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:8dyv, PDBe:8dyv, PDBj:8dyv
PDBsum8dyv
PubMed36692009
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)

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