Structure of PDB 5yew Chain A Binding Site BS01

Receptor Information
>5yew Chain A (length=390) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSPLKHFVLAKKAITAIFDQLLEFVTEGSHFVEATYKNPELDRIATEDDL
VEMQGYKDKLSIIGEVLSRRHMKVAFFGRTSSGKSSVINAMLWDKVLPSG
IGHITNCFLSVEGTDGDKAYLMTEGSDEKKSVKVNNQLAHALHMDKDLKA
GCLVRVFWPKAKCALLRDDLVLVDSPGTDVTTELDSWIDKFCLDADVFVL
VANSESTLMNTEKHFFHKVNERLSKPNIFILNNRWDASASEPEYMEDVRR
QHMERCLHFLVEELKVVNALEAQNRIFFVSAKEVLSARKQKAALAEGFHA
RLQEFQNFEQIFEECISQSAVKTKFEQHTIRAKQILATVKNIMDSVNLAA
EDLPKEIDQLEKIQNNSKLLRNKAVQLENELENFTKQFLP
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 chain5yew Chain A 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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PDB5yew Structural basis for GTP hydrolysis and conformational change of MFN1 in mediating membrane fusion
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S85 G87 K88 S89 S90 S103 G104 N237 R238 D240 S284 K286
Binding residue
(residue number reindexed from 1)		S81 G83 K84 S85 S86 S99 G100 N233 R234 D236 S280 K282
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0008053 mitochondrial fusion
Cellular Component
GO:0005741 mitochondrial outer membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yew, PDBe:5yew, PDBj:5yew
PDBsum5yew
PubMed29483649
UniProtQ8IWA4|MFN1_HUMAN Mitofusin-1 (Gene Name=MFN1)

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