Structure of PDB 4jyb Chain A Binding Site BS01

Receptor Information
>4jyb Chain A (length=323) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DMDTLRERLLAGDRAALARAITLAESRRADHRAAVRDLIDAVLPQTGRAI
RVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDK
TRMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETV
GVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGIFELADMIAVNKADDG
DGERRASAAASEYRAALHILTPPSATWTPPVVTISGLHGKGLDSLWSRIE
DHRSKLTATGEIAGKRREQDVKWMWALVHERLHQRLVGSAEVRQATAEAE
RAVAGGEHSPAAGADAIATLIGL
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain4jyb Chain A Residue 401 [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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PDB4jyb A switch III motif relays signaling between a B12 enzyme and its G-protein chaperone.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		P64 G65 G67 K68 S69 T70 N201 K202 D204 S241 L243
Binding residue
(residue number reindexed from 1)		P58 G59 G61 K62 S63 T64 N195 K196 D198 S235 L237
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.96,Kd=0.11uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0046872 metal ion binding
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4jyb, PDBe:4jyb, PDBj:4jyb
PDBsum4jyb
PubMed23873214
UniProtC5AP93

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