Structure of PDB 6b9d Chain A Binding Site BS01

Receptor Information
>6b9d Chain A (length=379) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFAK
GKSFLMDFMLRYMYNQESVDWVGNEPLTGFSTTGIQIWSEIFLINKPDGK
KVAVLLMDTQSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRL
AMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSQHEELQ
NVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILI
PWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYLPHPKSMLQATAEAN
NLAAVATAKDTYNKKMEEICGFLAPNDLQTKHLQLKEESVKLFRGVKKMG
GEEFSRRYLQQLESEIDELYIQYIKHNDS
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 chain6b9d Chain A Residue 501 [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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PDB6b9d A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		A77 K78 G79 K80 S81 F82 R217 D218 P272 V276 N279
Binding residue
(residue number reindexed from 1)		A49 K50 G51 K52 S53 F54 R168 D169 P221 V225 N228
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:6b9d, PDBe:6b9d, PDBj:6b9d
PDBsum6b9d
PubMed29180453
UniProtQ8WXF7|ATLA1_HUMAN Atlastin-1 (Gene Name=ATL1)

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