Structure of PDB 8dyv Chain A Binding Site BS04

Receptor Information

>8dyv Chain A (length=2549) Species: 9606 (Homo sapiens)

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 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: 8dyv Chain A Residue 4704

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dyv Structures of human dynein in complex with the lissencephaly 1 protein, LIS1.
• Resolution: 3.97 Å
• Binding residue (original residue number in PDB): L2909 V2910 G2940 A2941 G2942 K2943 T2944 T2945 W3097 R3174 N3650 E3652
• Binding residue (residue number reindexed from 1): L1167 V1168 G1198 A1199 G1200 K1201 T1202 T1203 W1355 R1432 N1650 E1652
• 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:8dyv, PDBe:8dyv, PDBj:8dyv
• PDBsum: 8dyv
• PubMed: 36692009
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)