Structure of PDB 6jfk Chain A Binding Site BS01

Receptor Information
>6jfk Chain A (length=428) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNASPLKHFVTAKKKINGIFEQLGAYIQESATFLEDTYRNAELDPVTTEE
QVLDVKGYLSKVRGISEVLARRHMKVAFFGRTSNGKSTVINAMLWDKVLP
SGIGHTTNCFLRVEGTDGHEAFLLTEGSEEKRSAKTVNQLAHALHQDKQL
HAGSLVSVMWPNSKCPLLKDDLVLMDSPGIDVTTELDSWIDKFCLDADVF
VLVANSESTLMQTEKHFFHKVSERLSRPNIFILNNRWDASASEPEYMEEV
RRQHMERCTSFLVDELGVVDRSQAGDRIFFVSAKEVLNARIQKAQGMPEG
GGALAEGFQVRMFEFQNFERRFEECISQSAVKTKFEQHTVRAKQIAEAVR
LIMDSLHMAAREQQVYCEEMREERQDRTRENLEQEIAAMNKKIEVLDSLQ
SKAKLLRNKAGWLDSELNMFTHQYLQPS
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 chain6jfk 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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PDB6jfk Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset.
Resolution1.997 Å
Binding residue
(original residue number in PDB)		S106 G108 K109 S110 T111 S124 I126 N258 R259 D261 S305 K307
Binding residue
(residue number reindexed from 1)		S83 G85 K86 S87 T88 S101 I103 N235 R236 D238 S282 K284
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=4.84,Kd=14.4uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6jfk, PDBe:6jfk, PDBj:6jfk
PDBsum6jfk
PubMed31664033
UniProtO95140|MFN2_HUMAN Mitofusin-2 (Gene Name=MFN2)

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