Structure of PDB 3vkh Chain A Binding Site BS04

Receptor Information
>3vkh Chain A (length=3042) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIYREVITAAQGEIALEEFLKGVREFWTTLELDLVNYQRKCKLVRGWDDL
FNKLAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDVQRR
WVYLEGIFINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAIERIQ
QTMERLSDLLGKVQKALGEYLERQRSAFARFYFVGDEDLLEIIGNSKDII
KIQKHFRKMFAGLANLTLDDEKTTIIGMSSAEGETVTFKKPISIANGPKI
HEWLTMVESEMKSTLATLLSESLQHFNQVDVNDHSKYSEWVDNYPTQLVL
LTSQIVWSTQVDQALGGGTLQQSKIQEQLQSIEQTTQMILNNLADSVLQD
LSAQKRKKFEHLITELVHQRDVVRQLQKCKNLTGNKDFDWLYHMRYYYDA
TQENVLHKLVIHMANATFYYGFEYLGIGERLVQTPLTDRCYLTLTQALES
RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGL
CQCGAWGCFDEFNRLEERILSAVSQQIQTIQVALKENSKEVELLNISLHQ
DMGIFVTMNPGYAGRSNLPDNLKKLFRSMAMIKPDREMIAQVMLYSQGFK
TAEVLAGKIVPLFKLCQEQLSAQSHYDFGLRALKSVLVSAGGIKRKCQPP
DAESKTKADQIYCQYEIGVLLNSINDTMIPKLVADDIPLIQSLLLDVFPG
SQLQPIQMDQLRKKIQEIAKQRHLVTKQEWVEKILQLHQILNINHGVMMV
GPSGGGKTTSWEVYLEAIEQVDNIKSEAHVMDPKAITKDQLFGSLDLTTR
EWTDGLFTATLRRIIDNVRGESTKRHWIIFDGDVDPEWVENLNSLLDDNK
LLTLPNGERLALPNNVRVMFEVQDLKYATLATISRCGMVWFSEEILTTQM
IFQNYLDTLSNEPFDPQEKEQQKRNENIPAGLKVQKECAAIISQYFEPGG
LVHKVLEDAGQRPHIMDFTRLRVLNSFFSLMNRSIVNVIEYNQLHSDFPM
SPENQSNYITNRLLYSLMWGLGGSMGLVERENFSKFIQTIAITPVPANTI
PLLDYSVSIDDANWSLWKNKVEVETHKVASPDVVIPTVDTTRHVDVLHAW
LSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKT
FDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTDKYGTQRVITFI
RQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHAPI
LLVDFPSTSSLTQIYGTFNRALMKLLPNLRSFADNLTDAMVEFYSESQKR
FTPDIQAHYIYSPRELSRWDRALLEAIQTMDGCTLEGLVRLWAHEALRLF
QDRLVETEEKEWTDKKIDEVALKHFPSVNLDALKRPILYSNWLTKDYQPV
NRSDLREYVKARLKVFYEEELDVPLVLFNEVLDHILRIDRVFRQPQGHAL
LIGVSGGGKSVLSRFVAWMNGLSIYTIKVNNNYKSSDFDDDLRMLLKRAG
CKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGLFEGEEFTALMHACK
ETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNPASPDFHNRSATSPA
LFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPPVFIQEAEILM
AIPPSHRDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTPRHYLDFINQV
VLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLAQKNRELDVKN
EQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAVQKVKAYADLE
KAEPAIIEAQEAVSTIKKKHLDEIKSLPKPPTPVKLAMEAVCLMLGGKKL
EWADIRKKIMEPNFITSIINYDTKKMMTPKIREAITKGYLEDPGFDYETV
NRASKACGPLVKWATAQTYYSEILKLKQDEIVATITALEKSIATYKEEYA
TLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQMST
VVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPSF
LSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMN
QYADKKITKTSFLDSSFMKNLESALRFGCPLLVQDVENIDPVLNPVLNKP
SFMIFLFTRDPTAHFTPDLCSRVTFVNFTVTPSSLQSQCLHEALKTERPD
THKKRSDLLKIQGEFQVKLRILEKSLLNALSQASGNILDDDSVISTLETL
KKETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEELSQFHL
YQFSLRAFLDIFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFNRVTRT
LLNDDKLTFALQLTIISVKGTSNEIEESEWDFLLKGGDNLTSIKETIPQL
DSLLSTTQQKWLICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPII
PESWIVAQAQLSNQQSTIVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGE
DFLNTQELDMANIVEKEVKSSSPLLLCSVPGYDASSKVDDLALQLHKQYK
SFAIGSPEGFELAEKSIYAAAKSGTWVLLKNIHLAPQWLVQLEKKLHSLS
PHPSFRLFMTSEIHPALPANLLRMSNVFSYENPPGVKANLLHTFIGIPAT
RMDKQPAERSRIYFLLAWFHAIIQERLRYIPLGWTKFFEFNDADLRGALD
SIDYWVDLYSKGRSNIDPDKIPWIAVRTILGSTIYGGRIDNEFDMRLLYS
FLEQLFTPSAFNPDFPLVPSIGLSVPEGTTRAHFMKWIEALPEISTPIWL
GLPENAESLLLSNKARKMINDLQKMQSSEESSSSEDKGKAKPLFRCFERE
ISTGGKLVKKITNDLANLLTNYLRSLTTSISKGIVPKEWKWYSVPETISL
SVWISDFSKRMQQLSEISESVWLGGLLNPEAYITATRQSASQLNGRLHAS
ASFNVKGMALEGAVWNNDQLTPTDILSTPISIATLTWKDPIFNNSSSKLS
VPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISSWKSD
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 chain3vkh Chain A Residue 9004 [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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PDB3vkh The 2.8 A crystal structure of the dynein motor domain
Resolution3.8 Å
Binding residue
(original residue number in PDB)		L2988 V2989 F2991 G3019 G3020 G3021 K3022 S3023 V3024 W3176
Binding residue
(residue number reindexed from 1)		L1425 V1426 F1428 G1456 G1457 G1458 K1459 S1460 V1461 W1613
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:3vkh, PDBe:3vkh, PDBj:3vkh
PDBsum3vkh
PubMed22398446
UniProtP34036|DYHC_DICDI Dynein heavy chain, cytoplasmic (Gene Name=dhcA)

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