Structure of PDB 8sz8 Chain b Binding Site BS01

Receptor Information
>8sz8 Chain b (length=692) 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
IVTTHIREREGRTKEQVMLLIDIELAYMNTNHEDFIIRKGWLTINNIGIM
KGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKH
IFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPEMDPQLE
RQVETIRNLVDSYMAIVNKTVRDLMPKTIMHLMINNTKEFIFSELLANLY
SCGDQNTLMEESAEQAQRRDEMLRMYHALKEALSIIGNINTT
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 chain8sz8 Chain b Residue 801 [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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PDB8sz8 Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission
Resolution3.55 Å
Binding residue
(original residue number in PDB)		G43 S45 S46 G60 T205 D208 L209 N236 R237 S238 Q239
Binding residue
(residue number reindexed from 1)		G35 S37 S38 G52 T197 D200 L201 N228 R229 S230 Q231
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:8sz8, PDBe:8sz8, PDBj:8sz8
PDBsum8sz8
PubMed38663399
UniProtQ05193|DYN1_HUMAN Dynamin-1 (Gene Name=DNM1)

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