Structure of PDB 5iqf Chain D Binding Site BS01

Receptor Information

>5iqf Chain D (length=301) Species: 1280 (Staphylococcus aureus)

RYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKT
KFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEI
KGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQN
VLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSC
NHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILR
MYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTY
K

Ligand information

• Ligand ID: GDP
• InChI: InChI=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
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=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 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(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
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 5iqf Chain D Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5iqf Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): I208 G211 D213 I224 K226 Y274 I277 F281 H379 I392 D393
• Binding residue (residue number reindexed from 1): I31 G34 D36 I47 K49 Y97 I100 F104 H202 I215 D216
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 2.3.1.-
  2.7.1.190: aminoglycoside 2''-phosphotransferase.

External links

• PDB: RCSB:5iqf, PDBe:5iqf, PDBj:5iqf
• PDBsum: 5iqf
• PubMed: 27161980
• UniProt: P0A0C1|AACA_STAAU Bifunctional AAC/APH (Gene Name=aacA-aphD)