Structure of PDB 6jsj Chain C Binding Site BS01

Receptor Information
>6jsj Chain C (length=619) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLNLTKQMIEIRTILNKVDSSSAHLTLPSIVVIGSQSSGKSSVLESIVGR
EFLPKGSRPIELTLVNTPNSNNVTADFPSMRLYNIKDFKEVKRMLMELNM
EEPIQLTIKSSRVPDLSLVDLPGYITKIRDLCEKYLTAPNIILAISAADV
DLANSSALKASKAADPKGLRTIGVITKLDLVDPEKARSILNNKKYPLSMG
YVGVITKTENTNGLKQIVSHQFEKAYFKENKKYFTNCQVSTKKLREKLIK
ILEISMSNALEPTSTLIQQELDDTSYLFKVEFNDRHLTPKSYLLNNIDVL
KLGIKEFQEKFHRNELKSILRAELDQKVLDVLATRYWKDDNLQDLSSSKL
ESDTDMLYWHKKLELASSGLTKMGIGRLSTMLTTNAILKELDNILESTQL
KNHELIKDLVSNTAINVLNSKYYSTADQVENCIKPFKYEIDLEERDWSLA
RQHSINLIKEELRQCNSRYQAIKNAVGSKKLANVMGYLENESKLLLERGS
EAIFLDKRCKVLSFRLKMLKNKCHSTIEKDRCPEVFLSAVSDKLTSTAVL
FLNVELLSDFFYNFPIELDRRLTLLGDEQVEMFAKEDPKISRHIELQKRK
ELLELALEKIDSILVFKKS
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 chain6jsj Chain C Residue 701 [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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PDB6jsj Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S37 S38 G39 K40 S41 S42 K203 I231 T232 K233
Binding residue
(residue number reindexed from 1)		S37 S38 G39 K40 S41 S42 K177 I205 T206 K207
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:6jsj, PDBe:6jsj, PDBj:6jsj
PDBsum6jsj
PubMed32041880
UniProtP32266|MGM1_YEAST Dynamin-like GTPase MGM1, mitochondrial (Gene Name=MGM1)

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