Structure of PDB 8dyu Chain A Binding Site BS04

Receptor Information

>8dyu Chain A (length=2562) Species: 9606 (Homo sapiens)

KHFKKMFAGVSSILGISSREGEEVMFKTPLVEKEMRVTLAKLLAESVTEV
EIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWSENVETALSSAAPLHS
VLSNVEVTLNVLADSVLMEQPPLRRRKLEHLITELVHQRDVTRSLIKSKI
DNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMANAKFNYGFEYLGVQDKLV
QTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALGHQLGRFVLVF
NCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQE
ALREHSNITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSL
AMTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFG
LRALKSVLVSAGNVKRERIQKIAENLPEQEILIQSVCETMVPKLVAEDIP
LLFSLLSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVE
KVLQLYQITQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIID
PKAISKDHLYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDG
DVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLAT
VSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQ
PYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNA
NHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTV
PLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDT
VRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSS
ATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKY
GTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLS
HRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMV
EFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRI
WAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPKAMSRPILYSNWLSK
DYIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQP
QGHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTV
LRRSGCKNEKIAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATL
MTQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRA
ATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVV
YDKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDF
INHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQNRSTALLKSLSAERE
RWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQ
QANIQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYP
LIIDPSGQATEFIMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQD
VESYDPVLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVE
FPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGE
FQLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEET
DIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYH
NVLYENPNVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARI
KLTYDAEFQHFLRGNGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIW
LDSSSPEQTVPYLWTPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNL
GESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQN
TQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKL
HSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSS
IPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLR
SACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQR
LLNTFLERLFTTRSFDSEFKLACDIQMPDGIRREEFVQWVELLPDTQTPS
WLGLPNNAERVLLTTQGVDMISKMLKMQTLHTTASNWLHLIPQTLSHLKR
IKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINE
LVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASKELKNI
HVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVFGVTGLKLQGAT
CNNNKLSLLPLTQLRWVKQSVVTLPVYLNFTRADLIFTVDFEIATKEDPR
SFYERGVAVLCT

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8dyu Chain A Residue 4704

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dyu Structures of human dynein in complex with the lissencephaly 1 protein, LIS1.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): L2909 S2939 G2940 A2941 G2942 K2943 T2944 T2945 W3097 R3174 L3177 N3650
• Binding residue (residue number reindexed from 1): L1180 S1210 G1211 A1212 G1213 K1214 T1215 T1216 W1368 R1445 L1448 N1663
• Annotation score: 5

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

External links

• PDB: RCSB:8dyu, PDBe:8dyu, PDBj:8dyu
• PDBsum: 8dyu
• PubMed: 36692009
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)