Structure of PDB 6ryk Chain A Binding Site BS01

Receptor Information

>6ryk Chain A (length=133) Species: 246197 (Myxococcus xanthus DK 1622)

SGRVTTVLLPLEKLQDESAFKLRPEGDVSGLATDIARLGQLFPVDVRPAG
EDRYQLVCGFRRVAALRFLKRDAVQARIHLRLSDEDALVMSLAEAIHATP
VGPEVLEAKRDELEAQGRLSAAVRDMLEKALAT

Ligand information

• Ligand ID: CTP
• InChI: InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: PCDQPRRSZKQHHS-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
• Formula: C9 H16 N3 O14 P3
• Name: CYTIDINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL223533
• DrugBank: DB02431
• ZINC: ZINC000003861746
• PDB chain: 6ryk Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ryk ParB-type DNA Segregation Proteins Are CTP-Dependent Molecular Switches.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): R311 L319 D322 I323 L329 F330 G347 F348 R349 R350
• Binding residue (residue number reindexed from 1): R23 L31 D34 I35 L41 F42 G59 F60 R61 R62
• Annotation score: 4

External links

• PDB: RCSB:6ryk, PDBe:6ryk, PDBj:6ryk
• PDBsum: 6ryk
• PubMed: 31835030
• UniProt: Q1D3H3|PADC_MYXXD ParBC domain-containing protein (Gene Name=padC)