Structure of PDB 8tym Chain f Binding Site BS01

Receptor Information
>8tym Chain f (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 chain8tym Chain f 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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PDB8tym Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.
Resolution3.58 Å
Binding residue
(original residue number in PDB)		S41 A42 G43 S45 S46 G60 T205 V235 N236
Binding residue
(residue number reindexed from 1)		S33 A34 G35 S37 S38 G52 T197 V227 N228
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
External links
PDB RCSB:8tym, PDBe:8tym, PDBj:8tym
PDBsum8tym
PubMed38663399
UniProtQ05193|DYN1_HUMAN Dynamin-1 (Gene Name=DNM1)

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