Structure of PDB 3vkg Chain A Binding Site BS03

Receptor Information
>3vkg Chain A (length=2954) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIDSLKETAWSAIIPAFDHAQNLIKIYLKGNAIITDLHSEAIKDRHWKIL
KKRLNTNWIITELTLGSIWDSDLARNENIYREVITAAQGEIALEEFLKGV
REFWTTLELDLVNYQRKCKLVRGWDDLFNKLAEHLNSISAMKMSPYYKVF
EEEANHWDDRLNKVRSLLDVWIDVQRRWVYLEGIFINQLLPAESTRFKSI
NSEFIAILKKVSGAPLILEVLAIERIQQTMERLSDLLGKVQKALGEYLER
QRSAFARFYFVGDEDLLEIIGNSKDIIKIQKHFRKMFAGLANLTLDDEKT
TIIGMSSAEGETVTFKKPISIANGPKIHEWLTMVESEMKSTLATLLSESL
QHFNQVDVNDHSKYSEWVDNYPTQLVLLTSQIVWSTQVDQALGGGTLQQS
KIQEQLQSIEQTTQMILNNLADSVLQDLSAQKRKKFEHLITELVHQRDVV
RQLQKCKNLTGNKDFDWLYHMRYYYDATQENVLHKLVIHMANATFYYGFE
YLGIGERLVQTPLTDRCYLTLTQALESRMGGNPFGPAGTGKTETVKALGS
QLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLEERILSAV
SQQIQTIQVALKENSKEVELLNISLHQDMGIFVTMNPGYAGRSNLPDNLK
KLFRSMAMIKPDREMIAQVMLYSQGFKTAEVLAGKIVPLFKLCQEQLSAQ
SHYDFGLRALKSVLVSAGGIKRKCQPPDAESKTKADQIYCQYEIGVLLNS
INDTMIPKLVADDIPLIQSLLLDVFPGSQLQPIQMDQLRKKIQEIAKQRH
LVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQVDN
IKSEAHVMDPKAITKDQLFGSLDLTTREWTDGLFTATLRRIIDNVRGEST
KRHWIIFDGDVDPEWVENLNSLLDDNKLLTLPNGERLALPNNVRVMFEVQ
DLKYATLATISRCGMVWFSEEILTTQMIFQNYLDTLSNEPFDPQEKEQQK
RNENAIPAGLKVQKECAAIISQYFEPGGLVHKVLEDAGQRPHIMDFTRLR
VLNSFFSLMNRSIVNVIEYNQLHSDFPMSPENQSNYITNRLLYSLMWGLG
GSMGLVERENFSKFIQTIAITPVPANTIPLLDYSVSIDDANWSLWKNKVE
VETHKVASPDVVIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLT
STLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQL
GKWLVVFCDEINLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDK
IQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIYGTFNRAL
MKLLPNLRSFADNLTDAMVEFYSESQKRFTPDIQAHYIYSPRELSRWDRA
LLEAIQTMDGCTLEGLVRLWAHEALRLFQDRLVETEEKEWTDKKIDEVAL
KHFPSVNLDALKRPILYSNWLTPVNRSDLREYVKARLKVFYPLVLFNEVL
DHILRIDRVFRQPQGHALLIGVSGGGKSVLSRFVAWMNGLSIYTIKYKSS
DFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMNTLLAGGEVPGL
FEGEEFTALMHACKETAQRNGLILDSEEELYKYFTSQVRRNLHVVFTMNP
ASPDFHNSPALFNRCVLDWFGEWSPEALFQVGSEFTRNLDLENPQYIAPP
VFIQEAEILMAIPPSHRDAVVSSLVYIHQTIGEANIRLLKRQGRQNYVTP
RHYLDFINQVVLLINEKRDQLEEEQLHLNIGLKKLRDTEAQVKDLQVSLA
QKNRELDVKNEQANQKLKQMVQDQQAAEIKQKDARELQVQLDVRNKEIAV
QKVKAYADLPLREEVEQLENAANELKLKQDEIVATITALEKSIATYKEEY
ATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSENFNTQMS
TVVGDVVLASAFLAYIGFFDQNFRTDLMRKWMIRLDSVGIKFKSDLSVPS
FLSKPEERLNWHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLM
NQYADKKITKTSFMKNLESALRFGCPLLVQDVESFMIFLFTRDPTAHFTP
DLCSRVTFVNFTVTPSSLQSQCLHEALKTERPDTHKKRSDLLKIQGEFQV
KLRILEKSLLNALSQASGNILDDDSVISTLETLKKETTEIALKVEETETV
MQEISEVSALYNPMALSCSRVYFAMEELSQFHLYQFSLRAFLDIFYNLLN
NNPNLVDKKDPNERLVYLSKDIFSMTFNRVTRTLLNDDKLTFALQLTIIS
VKGTSNEIEESEWDFLLKGGDNLTSIKETIPQLDSLLSTTQQKWLICLRQ
QVPSFSKLVDHIQQNSSDWKQFFGKDQVGEPIIPESWIVAQAQLSNQQST
IVSNFRKILLMKAFHSDRVLQYSHSFVCSVFGEDFLNTLDMANIVEKEVK
SSSPLLLCSVPGYDASSKVDDLALQLHKQYKSFAIGSPEGFELAEKSIYA
AAKSGTWVLLKNIHLAPQWLVQLEKKLHSLSPHPSFRLFMTSEIHPALPA
NLLRMSNVFSYENPPGVKANLLHTFIGIPATRMDKQPAERSRIYFLLAWF
HAIIQERLRYIPLGWTKFFEFNDADLRGALDSIDYWVDLYSKGRSNIDPD
KIPWIAVRTILGSTIYGGRIDNEFDMRLLYSFLEQLFTPSAFNPDFPLVP
SIGLSVPEGTTRAHFMKWIEALPEISTPIWLGLPENAESLLLSNKARKMI
NDLQKMQSSEEDSSSSEDKGKAKPLFRCFEREISTGGKLVKKITNDLANL
LKWYSVPETISLSVWISDFSKRMQQLSEISESVWLGGLLNPEAYITATRQ
SASQLNGRLHASASFNVKGMALEGAVWNNDQLTPTDILSTPISIATLTWK
DPIFNNSSSKLSVPVYLNETRSELLFSIDLPYDQSTSKQNWYQRSVSISS
WKSD
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 chain3vkg Chain A Residue 9003 [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]
PDB3vkg The 2.8 A crystal structure of the dynein motor domain
Resolution2.81 Å
Binding residue
(original residue number in PDB)		V2647 I2648 G2677 S2678 G2679 K2680 T2681 M2682 I2827 P2876 R2877 S2880
Binding residue
(residue number reindexed from 1)		V1162 I1163 G1192 S1193 G1194 K1195 T1196 M1197 I1342 P1391 R1392 S1395
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:3vkg, PDBe:3vkg, PDBj:3vkg
PDBsum3vkg
PubMed22398446
UniProtP34036|DYHC_DICDI Dynein heavy chain, cytoplasmic (Gene Name=dhcA)

[Back to BioLiP]