Structure of PDB 8fcy Chain A Binding Site BS03

Receptor Information
>8fcy Chain A (length=2864) Species: 9606,300852 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKLSPY
YKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHLLP
VETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQ
KALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVS
SIILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLVEKEMRVT
LAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWSENV
ETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLEHLI
TELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMA
NAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGK
TESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNR
LEERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQVKVSPDM
AIFITMNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAEVLANKIV
PFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQKIKREIAENLP
EQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQYHRGEMTALREEL
KKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGLMMVGPSGSGKSM
AWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLFTH
VLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGER
LSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARL
RSIPLSPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRC
LGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSG
DSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQ
IEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMT
LFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQ
LGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLE
RIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRA
MLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVR
GIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVA
LKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEE
LDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMN
GLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGF
LERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWF
TSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQ
VGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTL
HQANARLAKRGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVG
LRKIKETVDQVEELRRKVNRSTALLKSLSAERERWEKTSETFKNQMSTIA
GDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLS
NADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEY
KDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVR
RTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVT
RSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALN
EVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPL
STACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQ
RLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAE
FQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQAD
EQFGIWLDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAM
AHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGH
VEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPG
WLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVK
ANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKK
YEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGG
RVDNEFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREE
FVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQAWMRTLH
TTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDL
ADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSD
FSERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQA
NSWSLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAI
STALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKED
PRSFYERGVAVLCT
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 chain8fcy 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8fcy Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		V1113 V1114 G1143 S1144 G1145 K1146 T1147 M1148 I1292 P1341 R1342 T1345
Binding residue
(residue number reindexed from 1)		V1064 V1065 G1094 S1095 G1096 K1097 T1098 M1099 I1243 P1292 R1293 T1296
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:8fcy, PDBe:8fcy, PDBj:8fcy
PDBsum8fcy
PubMed37322240
UniProtQ14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1);
Q5SJX7

[Back to BioLiP]