Structure of PDB 8t0r Chain b Binding Site BS01

Receptor Information
>8t0r Chain b (length=693) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGASSVLENFVGRDFLP
RGSGIVTRRPLVLQLVNATTEYAEFLHCKGKKFTDFEEVRLEIEAETDRV
TGTNKGISPVPINLRVYSPHVLNLTLVDLPGMTKVPVGDQPPDIEFQIRD
MLMQFVTKENCLILAVSPANSDLANSDALKVAKEVDPQGQRTIGVITKLD
LMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAAERKF
FLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQLLSIE
KEVEEYKNFRPDDPARKTKALLQMVQQFAVDFEKRIEGSGDQIDTYELSG
GARINRIFHERFPFELVKMEFDEKELRREISYAIKNIHGIRTGLFTPDMA
FETIVKKQVKKIREPCLKCVDMVISELISTVRQCTKKLQQYPRLREEMER
IVTTHIREREGRTKEQVMLLIDIELAYMNTNHEDFIGIRKGWLTINNIGI
MKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSK
HIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPEMDPQL
ERQVETIRNLVDSYMAIVNKTVRDLMPKTIMHLMINNTKEFIFSELLANL
YSCGDQNTLMEESAEQAQRRDEMLRMYHALKEALSIIGNINTT
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8t0r Chain b Residue 901 [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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PDB8t0r Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission
Resolution3.97 Å
Binding residue
(original residue number in PDB)		S41 G43 S45 R59 G60 T205 D208 N236 Q239
Binding residue
(residue number reindexed from 1)		S33 G35 S37 R51 G52 T197 D200 N228 Q231
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding
GO:0008017 microtubule binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0019901 protein kinase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0007032 endosome organization
GO:0016185 synaptic vesicle budding from presynaptic endocytic zone membrane
GO:0031623 receptor internalization
GO:0048488 synaptic vesicle endocytosis
GO:0050804 modulation of chemical synaptic transmission
GO:0051260 protein homooligomerization
GO:0051289 protein homotetramerization
GO:0097494 regulation of vesicle size
GO:0099049 clathrin coat assembly involved in endocytosis
GO:0099050 vesicle scission
Cellular Component
GO:0001917 photoreceptor inner segment
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0030117 membrane coat
GO:0030139 endocytic vesicle
GO:0031410 cytoplasmic vesicle
GO:0042583 chromaffin granule
GO:0042995 cell projection
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0098684 photoreceptor ribbon synapse
GO:0098793 presynapse
GO:0098835 presynaptic endocytic zone membrane
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8t0r, PDBe:8t0r, PDBj:8t0r
PDBsum8t0r
PubMed38663399
UniProtQ05193|DYN1_HUMAN Dynamin-1 (Gene Name=DNM1)

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