Structure of PDB 8efr Chain P Binding Site BS01

Receptor Information
>8efr Chain P (length=766) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATDRGSESDKHFRKVSDKEKIDQLQEELLHTQLKYQRILERLEKENKELR
KLVLQKDDKGIHHRKLKKSLIDMYSEVLDVLSDYDASYNTQDHLPRVVVV
GDQSAGKTSVLEMIAQARIFPRGSGEMMTRSPVKVTLSEGPHHVALFKDS
SREFDLTKEEDLAALRHEIELRMRKNVKEGCTVSPETISLNVKGPGLQRM
VLVDLPGVINTVTSGMAPDTKETIFSISKAYMQNPNAIILCIQDGSVDAE
RSIVTDLVSQMDPHGRRTIFVLTKVDLAEKNVASPSRIQQIIEGKLFPMK
ALGYFAVVTGKGNSSESIEAIREYEEEFFQNSKLLKTSMLKAHQVTTRNL
SLAVSDCFWKMVRESVEQQADSFKATRFNLETEWKNNYPRLRELDRNELF
EKAKNEILDEVISLSQVTPKHWEEILQQSLWERVSTHVIENIYLPAAQTM
NSGTFNTTVDIKLKQWTDKQLPNKAVEVAWETLQEEFSRFMTEPKGKEHD
DIFDKLKEAVKEESIKRHKWNDFAEDSLRVIQHNALEDRSISDKQQWDAA
IYFMEEALQARLKDTENAIENMVGPDWKKRWLYWKNRTQEQCVHNETKNE
LEKMLKCNEEHPAYLASDEITTVRKNLESRGVEVDPSLIKDTWHQVYRRH
FLKTALNHCNLCRRGFYYYQRHFVDSELECNDVVLFWRIQRMLAITANTL
RQQLTNTEVRRLEKNVKEVLEDFAEDGEKKIKLLTGKRVQLAEDLKKVRE
IQEKLDAFIEALHQEK
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 chain8efr Chain P Residue 1001 [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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PDB8efr OPA1 helical structures give perspective to mitochondrial dysfunction.
Resolution5.48 Å
Binding residue
(original residue number in PDB)		A299 G300 T302 S303 P315 R316 G317 M322 T323 K468 G504 K505
Binding residue
(residue number reindexed from 1)		A105 G106 T108 S109 P121 R122 G123 M128 T129 K274 G310 K311
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:8efr, PDBe:8efr, PDBj:8efr
PDBsum8efr
PubMed37612506
UniProtO60313|OPA1_HUMAN Dynamin-like GTPase OPA1, mitochondrial (Gene Name=OPA1)

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