Structure of PDB 8tyn Chain c Binding Site BS01

Receptor Information
>8tyn Chain c (length=699) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGNRGMEDLIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGASSVLEN
FVGRDFLPRGSGIVTRRPLVLQLVNATTEYAEFLHCKGKKFTDFEEVRLE
IEAETDRVTGTNKGISPVPINLRVYSPHVLNLTLVDLPGMTKVPVGDQPP
DIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKVAKEVDPQGQRT
IGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITA
ALAAERKFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKL
QSQLLSIEKEVEEYKNFRPDDPARKTKALLQMVQQFAVDFEKRIEGSGDQ
IDTYELSGGARINRIFHERFPFELVKMEFDEKELRREISYAIKNIHGIRT
GLFTPDMAFETIVKKQVKKIREPCLKCVDMVISELISTVRQCTKKLQQYP
RLREEMERIVTTHIREREGRTKEQVMLLIDIELAYMNTNHEDFIGFIRKG
WLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRD
VEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAG
VYPEPQLERQVETIRNLVDSYMAIVNKTVRDLMPKTIMHLMINNTKEFIF
SELLANLYSCGDQNTLMEESAEQAQRRDEMLRMYHALKEALSIIGNINT
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 chain8tyn Chain c Residue 801 [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]
PDB8tyn Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.
Resolution3.26 Å
Binding residue
(original residue number in PDB)		S41 G43 A44 S45 R59 G60 K206 D208 N236 R237 S238 Q239 I242
Binding residue
(residue number reindexed from 1)		S41 G43 A44 S45 R59 G60 K206 D208 N236 R237 S238 Q239 I242
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
External links
PDB RCSB:8tyn, PDBe:8tyn, PDBj:8tyn
PDBsum8tyn
PubMed38663399
UniProtQ05193|DYN1_HUMAN Dynamin-1 (Gene Name=DNM1)

[Back to BioLiP]